PXD026474A_TPP_PSM <- rbind.data.frame(PXD026474A_1_TPP,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP$Spectrum))
PXD001684A_PD_PSM <- length(unique(paste0(PXD001684A_PD$File.ID,"_",PXD001684A_PD$First.Scan)))
PXD002266A_PD_PSM <- length(unique(paste0(PXD002266A_PD$File.ID,"_",PXD002266A_PD$First.Scan)))
PXD005207A_PD_PSM <- length(unique(paste0(PXD005207A_PD$File.ID,"_",PXD005207A_PD$First.Scan)))
PXD009157A_PD_PSM <- rbind.data.frame(PXD009157A_1_PD,PXD009157A_2_PD)
PXD009157A_PD_PSM <- length(unique(paste0(PXD009157A_PD$File.ID,"_",PXD009157A_PD$First.Scan)))
PXD009465A_PD_PSM <- length(unique(paste0(PXD009465A_PD$File.ID,"_",PXD009465A_PD$First.Scan)))
PXD026474A_PD_PSM <- length(unique(paste0(PXD026474A_PD$File.ID,"_",PXD026474A_PD$First.Scan)))
PXD001684A_MQ_PSM <- length(unique(paste0(PXD001684A_MQ$Spectrum,"_",PXD001684A_MQ$MS.MS.IDs)))
PXD002266A_MQ_PSM <- length(unique(paste0(PXD002266A_MQ$Spectrum,"_",PXD002266A_MQ$MS.MS.IDs)))
PXD005207A_MQ_PSM <- length(unique(paste0(PXD005207A_MQ$Spectrum,"_",PXD005207A_MQ$MS.MS.IDs)))
PXD009157A_MQ_PSM <- rbind.data.frame(PXD009157A_1_MQ,PXD009157A_2_MQ)
PXD009157A_MQ_PSM <- length(unique(paste0(PXD009157A_MQ$Spectrum,"_",PXD009157A_MQ$MS.MS.IDs)))
PXD009465A_MQ_PSM <- length(unique(paste0(PXD009465A_MQ$Spectrum,"_",PXD009465A_MQ$MS.MS.IDs)))
PXD026474A_MQ_PSM <- length(unique(paste0(PXD026474A_MQ$Spectrum,"_",PXD026474A_MQ$MS.MS.IDs)))
PXD001684A_TPP_PSM <- length(unique(PXD001684A_TPP$Spectrum))
PXD002266A_TPP_PSM <- length(unique(PXD002266A_TPP$Spectrum))
PXD005207A_TPP_PSM <- rbind.data.frame(PXD005207A_1_TPP,PXD005207A_2_TPP,PXD005207A_3_TPP,PXD005207A_4_TPP,PXD005207A_5_TPP,
PXD005207A_6_TPP,PXD005207A_7_TPP,PXD005207A_8_TPP,PXD005207A_9_TPP,PXD005207A_10_TPP,
PXD005207A_11_TPP)
PXD005207A_TPP_PSM <- length(unique(PXD005207A_TPP$Spectrum))
PXD009157A_TPP_PSM <- rbind.data.frame(PXD009157A_1_TPP,PXD009157A_2_TPP)
PXD009157A_TPP_PSM <- length(unique(PXD009157A_TPP$Spectrum))
PXD009465A_TPP_PSM <- length(unique(PXD009465A_TPP$Spectrum))
PXD026474A_TPP_PSM <- rbind.data.frame(PXD026474A_1_TPP,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP$Spectrum))
PXD001684A_TPP_PSM <- length(unique(PXD001684A_TPP$Spectrum))
PXD002266A_TPP_PSM <- length(unique(PXD002266A_TPP$Spectrum))
PXD005207A_TPP_PSM <- rbind.data.frame(PXD005207A_1_TPP,PXD005207A_2_TPP,PXD005207A_3_TPP,PXD005207A_4_TPP,PXD005207A_5_TPP,
PXD005207A_6_TPP,PXD005207A_7_TPP,PXD005207A_8_TPP,PXD005207A_9_TPP,PXD005207A_10_TPP,
PXD005207A_11_TPP)
PXD005207A_TPP_PSM <- length(unique(PXD005207A_TPP_PSM$Spectrum))
PXD009157A_TPP_PSM <- rbind.data.frame(PXD009157A_1_TPP,PXD009157A_2_TPP)
PXD009157A_TPP_PSM <- length(unique(PXD009157A_TPP_PSM$Spectrum))
PXD009465A_TPP_PSM <- length(unique(PXD009465A_TPP$Spectrum))
PXD026474A_TPP_PSM <- rbind.data.frame(PXD026474A_1_TPP_PSM,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP$Spectrum))
PXD001684A_PD_PSM <- length(unique(paste0(PXD001684A_PD$File.ID,"_",PXD001684A_PD$First.Scan)))
PXD002266A_PD_PSM <- length(unique(paste0(PXD002266A_PD$File.ID,"_",PXD002266A_PD$First.Scan)))
PXD005207A_PD_PSM <- length(unique(paste0(PXD005207A_PD$File.ID,"_",PXD005207A_PD$First.Scan)))
PXD009157A_PD_PSM <- rbind.data.frame(PXD009157A_1_PD,PXD009157A_2_PD)
PXD009157A_PD_PSM <- length(unique(paste0(PXD009157A_PD_PSM$File.ID,"_",PXD009157A_PD_PSM$First.Scan)))
PXD009465A_PD_PSM <- length(unique(paste0(PXD009465A_PD$File.ID,"_",PXD009465A_PD$First.Scan)))
PXD026474A_PD_PSM <- length(unique(paste0(PXD026474A_PD$File.ID,"_",PXD026474A_PD$First.Scan)))
PXD001684A_MQ_PSM <- length(unique(paste0(PXD001684A_MQ$Spectrum,"_",PXD001684A_MQ$MS.MS.IDs)))
PXD002266A_MQ_PSM <- length(unique(paste0(PXD002266A_MQ$Spectrum,"_",PXD002266A_MQ$MS.MS.IDs)))
PXD005207A_MQ_PSM <- length(unique(paste0(PXD005207A_MQ$Spectrum,"_",PXD005207A_MQ$MS.MS.IDs)))
PXD009157A_MQ_PSM <- rbind.data.frame(PXD009157A_1_MQ,PXD009157A_2_MQ)
PXD009157A_MQ_PSM <- length(unique(paste0(PXD009157A_MQ_PSM$Spectrum,"_",PXD009157A_MQ_PSM$MS.MS.IDs)))
PXD009465A_MQ_PSM <- length(unique(paste0(PXD009465A_MQ$Spectrum,"_",PXD009465A_MQ$MS.MS.IDs)))
PXD026474A_MQ_PSM <- length(unique(paste0(PXD026474A_MQ$Spectrum,"_",PXD026474A_MQ$MS.MS.IDs)))
PXD001684A_TPP_PSM <- length(unique(PXD001684A_TPP$Spectrum))
PXD002266A_TPP_PSM <- length(unique(PXD002266A_TPP$Spectrum))
PXD005207A_TPP_PSM <- rbind.data.frame(PXD005207A_1_TPP,PXD005207A_2_TPP,PXD005207A_3_TPP,PXD005207A_4_TPP,PXD005207A_5_TPP,
PXD005207A_6_TPP,PXD005207A_7_TPP,PXD005207A_8_TPP,PXD005207A_9_TPP,PXD005207A_10_TPP,
PXD005207A_11_TPP)
PXD005207A_TPP_PSM <- length(unique(PXD005207A_TPP_PSM$Spectrum))
PXD009157A_TPP_PSM <- rbind.data.frame(PXD009157A_1_TPP,PXD009157A_2_TPP)
PXD009157A_TPP_PSM <- length(unique(PXD009157A_TPP_PSM$Spectrum))
PXD009465A_TPP_PSM <- length(unique(PXD009465A_TPP$Spectrum))
PXD026474A_TPP_PSM <- rbind.data.frame(PXD026474A_1_TPP_PSM,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP_PSM$Spectrum))
PXD001684A_TPP_PSM <- length(unique(PXD001684A_TPP$Spectrum))
PXD002266A_TPP_PSM <- length(unique(PXD002266A_TPP$Spectrum))
PXD005207A_TPP_PSM <- rbind.data.frame(PXD005207A_1_TPP,PXD005207A_2_TPP,PXD005207A_3_TPP,PXD005207A_4_TPP,PXD005207A_5_TPP,
PXD005207A_6_TPP,PXD005207A_7_TPP,PXD005207A_8_TPP,PXD005207A_9_TPP,PXD005207A_10_TPP,
PXD005207A_11_TPP)
PXD005207A_TPP_PSM <- length(unique(PXD005207A_TPP_PSM$Spectrum))
PXD009157A_TPP_PSM <- rbind.data.frame(PXD009157A_1_TPP,PXD009157A_2_TPP)
PXD009157A_TPP_PSM <- length(unique(PXD009157A_TPP_PSM$Spectrum))
PXD009465A_TPP_PSM <- length(unique(PXD009465A_TPP$Spectrum))
PXD026474A_TPP_PSM <- rbind.data.frame(PXD026474A_TPP_PSM,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP_PSM$Spectrum))
PXD001684A_PD_PSM <- length(unique(paste0(PXD001684A_PD$File.ID,"_",PXD001684A_PD$First.Scan)))
PXD002266A_PD_PSM <- length(unique(paste0(PXD002266A_PD$File.ID,"_",PXD002266A_PD$First.Scan)))
PXD005207A_PD_PSM <- length(unique(paste0(PXD005207A_PD$File.ID,"_",PXD005207A_PD$First.Scan)))
PXD009157A_PD_PSM <- rbind.data.frame(PXD009157A_1_PD,PXD009157A_2_PD)
PXD009157A_PD_PSM <- length(unique(paste0(PXD009157A_PD_PSM$File.ID,"_",PXD009157A_PD_PSM$First.Scan)))
PXD009465A_PD_PSM <- length(unique(paste0(PXD009465A_PD$File.ID,"_",PXD009465A_PD$First.Scan)))
PXD026474A_PD_PSM <- length(unique(paste0(PXD026474A_PD$File.ID,"_",PXD026474A_PD$First.Scan)))
PXD001684A_MQ_PSM <- length(unique(paste0(PXD001684A_MQ$Spectrum,"_",PXD001684A_MQ$MS.MS.IDs)))
PXD002266A_MQ_PSM <- length(unique(paste0(PXD002266A_MQ$Spectrum,"_",PXD002266A_MQ$MS.MS.IDs)))
PXD005207A_MQ_PSM <- length(unique(paste0(PXD005207A_MQ$Spectrum,"_",PXD005207A_MQ$MS.MS.IDs)))
PXD009157A_MQ_PSM <- rbind.data.frame(PXD009157A_1_MQ,PXD009157A_2_MQ)
PXD009157A_MQ_PSM <- length(unique(paste0(PXD009157A_MQ_PSM$Spectrum,"_",PXD009157A_MQ_PSM$MS.MS.IDs)))
PXD009465A_MQ_PSM <- length(unique(paste0(PXD009465A_MQ$Spectrum,"_",PXD009465A_MQ$MS.MS.IDs)))
PXD026474A_MQ_PSM <- length(unique(paste0(PXD026474A_MQ$Spectrum,"_",PXD026474A_MQ$MS.MS.IDs)))
PXD001684A_TPP_PSM <- length(unique(PXD001684A_TPP$Spectrum))
PXD002266A_TPP_PSM <- length(unique(PXD002266A_TPP$Spectrum))
PXD005207A_TPP<- rbind.data.frame(PXD005207A_1_TPP,PXD005207A_2_TPP,PXD005207A_3_TPP,PXD005207A_4_TPP,PXD005207A_5_TPP,
PXD005207A_6_TPP,PXD005207A_7_TPP,PXD005207A_8_TPP,PXD005207A_9_TPP,PXD005207A_10_TPP,
PXD005207A_11_TPP)
PXD005207A_TPP_PSM <- length(unique(PXD005207A_TPP$Spectrum))
PXD009157A_TPP <- rbind.data.frame(PXD009157A_1_TPP,PXD009157A_2_TPP)
PXD009157A_TPP_PSM <- length(unique(PXD009157A_TPP$Spectrum))
PXD009465A_TPP_PSM <- length(unique(PXD009465A_TPP$Spectrum))
PXD026474A_TPP <- rbind.data.frame(PXD026474A_TPP_PSM,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP$Spectrum))
PXD001684A_TPP_PSM <- length(unique(PXD001684A_TPP$Spectrum))
PXD002266A_TPP_PSM <- length(unique(PXD002266A_TPP$Spectrum))
PXD005207A_TPP<- rbind.data.frame(PXD005207A_1_TPP,PXD005207A_2_TPP,PXD005207A_3_TPP,PXD005207A_4_TPP,PXD005207A_5_TPP,
PXD005207A_6_TPP,PXD005207A_7_TPP,PXD005207A_8_TPP,PXD005207A_9_TPP,PXD005207A_10_TPP,
PXD005207A_11_TPP)
PXD005207A_TPP_PSM <- length(unique(PXD005207A_TPP$Spectrum))
PXD009157A_TPP <- rbind.data.frame(PXD009157A_1_TPP,PXD009157A_2_TPP)
PXD009157A_TPP_PSM <- length(unique(PXD009157A_TPP$Spectrum))
PXD009465A_TPP_PSM <- length(unique(PXD009465A_TPP$Spectrum))
PXD026474A_TPP <- rbind.data.frame(PXD026474A_TPP_PSM,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP$Spectrum))
PXD001684A_PD_PSM <- length(unique(paste0(PXD001684A_PD$File.ID,"_",PXD001684A_PD$First.Scan)))
PXD002266A_PD_PSM <- length(unique(paste0(PXD002266A_PD$File.ID,"_",PXD002266A_PD$First.Scan)))
PXD005207A_PD_PSM <- length(unique(paste0(PXD005207A_PD$File.ID,"_",PXD005207A_PD$First.Scan)))
PXD009157A_PD <- rbind.data.frame(PXD009157A_1_PD,PXD009157A_2_PD)
PXD009157A_PD_PSM <- length(unique(paste0(PXD009157A_PD$File.ID,"_",PXD009157A_PD$First.Scan)))
PXD009465A_PD_PSM <- length(unique(paste0(PXD009465A_PD$File.ID,"_",PXD009465A_PD$First.Scan)))
PXD026474A_PD_PSM <- length(unique(paste0(PXD026474A_PD$File.ID,"_",PXD026474A_PD$First.Scan)))
PXD001684A_MQ_PSM <- length(unique(paste0(PXD001684A_MQ$Spectrum,"_",PXD001684A_MQ$MS.MS.IDs)))
PXD002266A_MQ_PSM <- length(unique(paste0(PXD002266A_MQ$Spectrum,"_",PXD002266A_MQ$MS.MS.IDs)))
PXD005207A_MQ_PSM <- length(unique(paste0(PXD005207A_MQ$Spectrum,"_",PXD005207A_MQ$MS.MS.IDs)))
PXD009157A_MQ <- rbind.data.frame(PXD009157A_1_MQ,PXD009157A_2_MQ)
PXD009157A_MQ_PSM <- length(unique(paste0(PXD009157A_MQ$Spectrum,"_",PXD009157A_MQ$MS.MS.IDs)))
PXD009465A_MQ_PSM <- length(unique(paste0(PXD009465A_MQ$Spectrum,"_",PXD009465A_MQ$MS.MS.IDs)))
PXD026474A_MQ_PSM <- length(unique(paste0(PXD026474A_MQ$Spectrum,"_",PXD026474A_MQ$MS.MS.IDs)))
Unique_PXD001684A_TPP <- cbind.data.frame(distinct(PXD001684A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD002266A_TPP <- cbind.data.frame(distinct(PXD002266A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD005207A_TPP <- cbind.data.frame(distinct(PXD005207A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD009157A_TPP <- cbind.data.frame(distinct(PXD009157A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD009465A_TPP <- cbind.data.frame(distinct(PXD009465A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD026474A_TPP <- cbind.data.frame(distinct(PXD026474A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD001684A_PD <- cbind.data.frame(distinct(PXD001684A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD002266A_PD <- cbind.data.frame(distinct(PXD002266A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD005207A_PD <- cbind.data.frame(distinct(PXD005207A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD009157A_PD <- cbind.data.frame(distinct(PXD009157A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD009465A_PD <- cbind.data.frame(distinct(PXD009465A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD026474A_PD <- cbind.data.frame(distinct(PXD026474A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD001684A_MQ <- cbind.data.frame(distinct(PXD001684A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD002266A_MQ <- cbind.data.frame(distinct(PXD002266A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD005207A_MQ <- cbind.data.frame(distinct(PXD005207A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD009157A_MQ <- cbind.data.frame(distinct(PXD009157A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD009465A_MQ <- cbind.data.frame(distinct(PXD009465A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD026474A_MQ <- cbind.data.frame(distinct(PXD026474A_MQ,Seq_nPhospho),pipeline="MQ")
M1_PXD001684A <- merge(Unique_PXD001684A_TPP,Unique_PXD001684A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD001684A <- merge(M1_PXD001684A,Unique_PXD001684A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD002266A <- merge(Unique_PXD002266A_TPP,Unique_PXD002266A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD002266A <- merge(M1_PXD002266A,Unique_PXD002266A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD005207A <- merge(Unique_PXD005207A_TPP,Unique_PXD005207A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD005207A <- merge(M1_PXD005207A,Unique_PXD005207A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD009157A <- merge(Unique_PXD009157A_TPP,Unique_PXD009157A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD009157A <- merge(M1_PXD009157A,Unique_PXD009157A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD009465A <- merge(Unique_PXD009465A_TPP,Unique_PXD009465A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD009465A <- merge(M1_PXD009465A,Unique_PXD009465A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD026474A <- merge(Unique_PXD026474A_TPP,Unique_PXD026474A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD026474A <- merge(M1_PXD026474A,Unique_PXD026474A_MQ, by="Seq_nPhospho", all = TRUE)
Merged_PXD001684A$Group <- paste0(Merged_PXD001684A$pipeline.x,"_",Merged_PXD001684A$pipeline.y,"_",Merged_PXD001684A$pipeline)
Merged_PXD001684A$Group <- gsub('_NA', '', Merged_PXD001684A$Group)
Merged_PXD001684A$Group <- gsub('NA_', '', Merged_PXD001684A$Group)
Merged_PXD002266A$Group <- paste0(Merged_PXD002266A$pipeline.x,"_",Merged_PXD002266A$pipeline.y,"_",Merged_PXD002266A$pipeline)
Merged_PXD002266A$Group <- gsub('_NA', '', Merged_PXD002266A$Group)
Merged_PXD002266A$Group <- gsub('NA_', '', Merged_PXD002266A$Group)
Merged_PXD005207A$Group <- paste0(Merged_PXD005207A$pipeline.x,"_",Merged_PXD005207A$pipeline.y,"_",Merged_PXD005207A$pipeline)
Merged_PXD005207A$Group <- gsub('_NA', '', Merged_PXD005207A$Group)
Merged_PXD005207A$Group <- gsub('NA_', '', Merged_PXD005207A$Group)
Merged_PXD009157A$Group <- paste0(Merged_PXD009157A$pipeline.x,"_",Merged_PXD009157A$pipeline.y,"_",Merged_PXD009157A$pipeline)
Merged_PXD009157A$Group <- gsub('_NA', '', Merged_PXD009157A$Group)
Merged_PXD009157A$Group <- gsub('NA_', '', Merged_PXD009157A$Group)
Merged_PXD009465A$Group <- paste0(Merged_PXD009465A$pipeline.x,"_",Merged_PXD009465A$pipeline.y,"_",Merged_PXD009465A$pipeline)
Merged_PXD009465A$Group <- gsub('_NA', '', Merged_PXD009465A$Group)
Merged_PXD009465A$Group <- gsub('NA_', '', Merged_PXD009465A$Group)
Merged_PXD026474A$Group <- paste0(Merged_PXD026474A$pipeline.x,"_",Merged_PXD026474A$pipeline.y,"_",Merged_PXD026474A$pipeline)
Merged_PXD026474A$Group <- gsub('_NA', '', Merged_PXD026474A$Group)
Merged_PXD026474A$Group <- gsub('NA_', '', Merged_PXD026474A$Group)
tab1(Merged_PXD001684A$Group)
tab1(Merged_PXD002266A$Group)
tab1(Merged_PXD005207A$Group)
tab1(Merged_PXD009157A$Group)
tab1(Merged_PXD009465A$Group)
tab1(Merged_PXD026474A$Group)
# Supp Table 2 - Comparing PSM + Number of phosphorylations across data sets #
##############################################################################
#> [conflicted] Will prefer dplyr::filter over any other package
suppressPackageStartupMessages(library("tidyverse"))
library(dplyr)
library(stringr)
library(useful)
library(MASS)
library(reshape2)
library(epiDisplay)
PXD001684A_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD001684.csv')
PXD002266A_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD002266.csv')
PXD005207A_1_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_Plasmo.csv')
PXD005207A_2_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_Plfalci.csv')
PXD005207A_3_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigMix.csv')
PXD005207A_4_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR1.csv')
PXD005207A_5_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR2.csv')
PXD005207A_6_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR3.csv')
PXD005207A_7_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR4.csv')
PXD005207A_8_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR5.csv')
PXD005207A_9_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_StageR1.csv')
PXD005207A_10_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_StageR4.csv')
PXD005207A_11_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_StageR5.csv')
PXD009157A_1_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD009157_1.csv')
PXD009157A_2_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD009157_2.csv')
PXD009465A_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD009465.csv')
PXD026474A_1_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD026474_KO.csv')
PXD026474A_2_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD026474_WT.csv')
PXD001684A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD001684_A_PSMSITE.csv')
PXD002266A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD002266_A_PSMSITE.csv')
PXD005207A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD005207_A_PSMSITE.csv')
PXD009157A_1_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD009157_1_A_PSMSITE.csv')
PXD009157A_2_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD009157_2_A_PSMSITE.csv')
PXD009465A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD009465_A_PSMSITE.csv')
PXD026474A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD026474_A_PSMSITE.csv')
PXD001684A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD001684A_PSMSITE.csv')
PXD002266A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD002266A_PSMSITE.csv')
PXD005207A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD005207A_PSMSITE.csv')
PXD009157A_1_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD009157A_1_PSMSITE.csv')
PXD009157A_2_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD009157A_2_PSMSITE.csv')
PXD009465A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD009465A_PSMSITE.csv')
PXD026474A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD026474A_PSMSITE.csv')
PXD001684A_TPP$Seq_nPhospho <- paste0(PXD001684A_TPP$Peptide,"_",str_count(PXD001684A_TPP$Peptide_mod,"Phospho"))
PXD002266A_TPP$Seq_nPhospho <- paste0(PXD002266A_TPP$Peptide,"_",str_count(PXD002266A_TPP$Peptide_mod,"Phospho"))
PXD005207A_1_TPP$Seq_nPhospho <- paste0(PXD005207A_1_TPP$Peptide,"_",str_count(PXD005207A_1_TPP$Peptide_mod,"Phospho"))
PXD005207A_2_TPP$Seq_nPhospho <- paste0(PXD005207A_2_TPP$Peptide,"_",str_count(PXD005207A_2_TPP$Peptide_mod,"Phospho"))
PXD005207A_3_TPP$Seq_nPhospho <- paste0(PXD005207A_3_TPP$Peptide,"_",str_count(PXD005207A_3_TPP$Peptide_mod,"Phospho"))
PXD005207A_4_TPP$Seq_nPhospho <- paste0(PXD005207A_4_TPP$Peptide,"_",str_count(PXD005207A_4_TPP$Peptide_mod,"Phospho"))
PXD005207A_5_TPP$Seq_nPhospho <- paste0(PXD005207A_5_TPP$Peptide,"_",str_count(PXD005207A_5_TPP$Peptide_mod,"Phospho"))
PXD005207A_6_TPP$Seq_nPhospho <- paste0(PXD005207A_6_TPP$Peptide,"_",str_count(PXD005207A_6_TPP$Peptide_mod,"Phospho"))
PXD005207A_7_TPP$Seq_nPhospho <- paste0(PXD005207A_7_TPP$Peptide,"_",str_count(PXD005207A_7_TPP$Peptide_mod,"Phospho"))
PXD005207A_8_TPP$Seq_nPhospho <- paste0(PXD005207A_8_TPP$Peptide,"_",str_count(PXD005207A_8_TPP$Peptide_mod,"Phospho"))
PXD005207A_9_TPP$Seq_nPhospho <- paste0(PXD005207A_9_TPP$Peptide,"_",str_count(PXD005207A_9_TPP$Peptide_mod,"Phospho"))
PXD005207A_10_TPP$Seq_nPhospho <- paste0(PXD005207A_10_TPP$Peptide,"_",str_count(PXD005207A_10_TPP$Peptide_mod,"Phospho"))
PXD005207A_11_TPP$Seq_nPhospho <- paste0(PXD005207A_11_TPP$Peptide,"_",str_count(PXD005207A_11_TPP$Peptide_mod,"Phospho"))
PXD009157A_1_TPP$Seq_nPhospho <- paste0(PXD009157A_1_TPP$Peptide,"_",str_count(PXD009157A_1_TPP$Peptide_mod,"Phospho"))
PXD009157A_2_TPP$Seq_nPhospho <- paste0(PXD009157A_2_TPP$Peptide,"_",str_count(PXD009157A_2_TPP$Peptide_mod,"Phospho"))
PXD009465A_TPP$Seq_nPhospho <- paste0(PXD009465A_TPP$Peptide,"_",str_count(PXD009465A_TPP$Peptide_mod,"Phospho"))
PXD026474A_1_TPP$Seq_nPhospho <- paste0(PXD026474A_1_TPP$Peptide,"_",str_count(PXD026474A_1_TPP$Peptide_mod,"Phospho"))
PXD026474A_2_TPP$Seq_nPhospho <- paste0(PXD026474A_2_TPP$Peptide,"_",str_count(PXD026474A_2_TPP$Peptide_mod,"Phospho"))
PXD001684A_PD$Seq_nPhospho <- paste0(PXD001684A_PD$Sequence,"_",PXD001684A_PD$n_Phos)
PXD002266A_PD$Seq_nPhospho <- paste0(PXD002266A_PD$Sequence,"_",PXD002266A_PD$n_Phos)
PXD005207A_PD$Seq_nPhospho <- paste0(PXD005207A_PD$Sequence,"_",PXD005207A_PD$n_Phos)
PXD009157A_1_PD$Seq_nPhospho <- paste0(PXD009157A_1_PD$Sequence,"_",PXD009157A_1_PD$n_Phos)
PXD009157A_2_PD$Seq_nPhospho <- paste0(PXD009157A_2_PD$Sequence,"_",PXD009157A_2_PD$n_Phos)
PXD009465A_PD$Seq_nPhospho <- paste0(PXD009465A_PD$Sequence,"_",PXD009465A_PD$n_Phos)
PXD026474A_PD$Seq_nPhospho <- paste0(PXD026474A_PD$Sequence,"_",PXD026474A_PD$n_Phos)
PXD001684A_MQ$Seq_nPhospho <- paste0(PXD001684A_MQ$Sequence,"_",str_count(PXD001684A_MQ$Modified.sequence,"Phospho"))
PXD002266A_MQ$Seq_nPhospho <- paste0(PXD002266A_MQ$Sequence,"_",str_count(PXD002266A_MQ$Modified.sequence,"Phospho"))
PXD005207A_MQ$Seq_nPhospho <- paste0(PXD005207A_MQ$Sequence,"_",str_count(PXD005207A_MQ$Modified.sequence,"Phospho"))
PXD009157A_1_MQ$Seq_nPhospho <- paste0(PXD009157A_1_MQ$Sequence,"_",str_count(PXD009157A_1_MQ$Modified.sequence,"Phospho"))
PXD009157A_2_MQ$Seq_nPhospho <- paste0(PXD009157A_2_MQ$Sequence,"_",str_count(PXD009157A_2_MQ$Modified.sequence,"Phospho"))
PXD009465A_MQ$Seq_nPhospho <- paste0(PXD009465A_MQ$Sequence,"_",str_count(PXD009465A_MQ$Modified.sequence,"Phospho"))
PXD026474A_MQ$Seq_nPhospho <- paste0(PXD026474A_MQ$Sequence,"_",str_count(PXD026474A_MQ$Modified.sequence,"Phospho"))
# PSM count at 1% FDR #
PXD001684A_TPP_PSM <- length(unique(PXD001684A_TPP$Spectrum))
PXD002266A_TPP_PSM <- length(unique(PXD002266A_TPP$Spectrum))
PXD005207A_TPP<- rbind.data.frame(PXD005207A_1_TPP,PXD005207A_2_TPP,PXD005207A_3_TPP,PXD005207A_4_TPP,PXD005207A_5_TPP,
PXD005207A_6_TPP,PXD005207A_7_TPP,PXD005207A_8_TPP,PXD005207A_9_TPP,PXD005207A_10_TPP,
PXD005207A_11_TPP)
PXD005207A_TPP_PSM <- length(unique(PXD005207A_TPP$Spectrum))
PXD009157A_TPP <- rbind.data.frame(PXD009157A_1_TPP,PXD009157A_2_TPP)
PXD009157A_TPP_PSM <- length(unique(PXD009157A_TPP$Spectrum))
PXD009465A_TPP_PSM <- length(unique(PXD009465A_TPP$Spectrum))
PXD026474A_TPP <- rbind.data.frame(PXD026474A_TPP_PSM,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP$Spectrum))
PXD001684A_PD_PSM <- length(unique(paste0(PXD001684A_PD$File.ID,"_",PXD001684A_PD$First.Scan)))
PXD002266A_PD_PSM <- length(unique(paste0(PXD002266A_PD$File.ID,"_",PXD002266A_PD$First.Scan)))
PXD005207A_PD_PSM <- length(unique(paste0(PXD005207A_PD$File.ID,"_",PXD005207A_PD$First.Scan)))
PXD009157A_PD <- rbind.data.frame(PXD009157A_1_PD,PXD009157A_2_PD)
PXD009157A_PD_PSM <- length(unique(paste0(PXD009157A_PD$File.ID,"_",PXD009157A_PD$First.Scan)))
PXD009465A_PD_PSM <- length(unique(paste0(PXD009465A_PD$File.ID,"_",PXD009465A_PD$First.Scan)))
PXD026474A_PD_PSM <- length(unique(paste0(PXD026474A_PD$File.ID,"_",PXD026474A_PD$First.Scan)))
PXD001684A_MQ_PSM <- length(unique(paste0(PXD001684A_MQ$Spectrum,"_",PXD001684A_MQ$MS.MS.IDs)))
PXD002266A_MQ_PSM <- length(unique(paste0(PXD002266A_MQ$Spectrum,"_",PXD002266A_MQ$MS.MS.IDs)))
PXD005207A_MQ_PSM <- length(unique(paste0(PXD005207A_MQ$Spectrum,"_",PXD005207A_MQ$MS.MS.IDs)))
PXD009157A_MQ <- rbind.data.frame(PXD009157A_1_MQ,PXD009157A_2_MQ)
PXD009157A_MQ_PSM <- length(unique(paste0(PXD009157A_MQ$Spectrum,"_",PXD009157A_MQ$MS.MS.IDs)))
PXD009465A_MQ_PSM <- length(unique(paste0(PXD009465A_MQ$Spectrum,"_",PXD009465A_MQ$MS.MS.IDs)))
PXD026474A_MQ_PSM <- length(unique(paste0(PXD026474A_MQ$Spectrum,"_",PXD026474A_MQ$MS.MS.IDs)))
# Unique PSMs + nPhospho
Unique_PXD001684A_TPP <- cbind.data.frame(distinct(PXD001684A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD002266A_TPP <- cbind.data.frame(distinct(PXD002266A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD005207A_TPP <- cbind.data.frame(distinct(PXD005207A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD009157A_TPP <- cbind.data.frame(distinct(PXD009157A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD009465A_TPP <- cbind.data.frame(distinct(PXD009465A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD026474A_TPP <- cbind.data.frame(distinct(PXD026474A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD001684A_PD <- cbind.data.frame(distinct(PXD001684A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD002266A_PD <- cbind.data.frame(distinct(PXD002266A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD005207A_PD <- cbind.data.frame(distinct(PXD005207A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD009157A_PD <- cbind.data.frame(distinct(PXD009157A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD009465A_PD <- cbind.data.frame(distinct(PXD009465A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD026474A_PD <- cbind.data.frame(distinct(PXD026474A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD001684A_MQ <- cbind.data.frame(distinct(PXD001684A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD002266A_MQ <- cbind.data.frame(distinct(PXD002266A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD005207A_MQ <- cbind.data.frame(distinct(PXD005207A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD009157A_MQ <- cbind.data.frame(distinct(PXD009157A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD009465A_MQ <- cbind.data.frame(distinct(PXD009465A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD026474A_MQ <- cbind.data.frame(distinct(PXD026474A_MQ,Seq_nPhospho),pipeline="MQ")
# Merging data #
################
M1_PXD001684A <- merge(Unique_PXD001684A_TPP,Unique_PXD001684A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD001684A <- merge(M1_PXD001684A,Unique_PXD001684A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD002266A <- merge(Unique_PXD002266A_TPP,Unique_PXD002266A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD002266A <- merge(M1_PXD002266A,Unique_PXD002266A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD005207A <- merge(Unique_PXD005207A_TPP,Unique_PXD005207A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD005207A <- merge(M1_PXD005207A,Unique_PXD005207A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD009157A <- merge(Unique_PXD009157A_TPP,Unique_PXD009157A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD009157A <- merge(M1_PXD009157A,Unique_PXD009157A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD009465A <- merge(Unique_PXD009465A_TPP,Unique_PXD009465A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD009465A <- merge(M1_PXD009465A,Unique_PXD009465A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD026474A <- merge(Unique_PXD026474A_TPP,Unique_PXD026474A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD026474A <- merge(M1_PXD026474A,Unique_PXD026474A_MQ, by="Seq_nPhospho", all = TRUE)
Merged_PXD001684A$Group <- paste0(Merged_PXD001684A$pipeline.x,"_",Merged_PXD001684A$pipeline.y,"_",Merged_PXD001684A$pipeline)
Merged_PXD001684A$Group <- gsub('_NA', '', Merged_PXD001684A$Group)
Merged_PXD001684A$Group <- gsub('NA_', '', Merged_PXD001684A$Group)
Merged_PXD002266A$Group <- paste0(Merged_PXD002266A$pipeline.x,"_",Merged_PXD002266A$pipeline.y,"_",Merged_PXD002266A$pipeline)
Merged_PXD002266A$Group <- gsub('_NA', '', Merged_PXD002266A$Group)
Merged_PXD002266A$Group <- gsub('NA_', '', Merged_PXD002266A$Group)
Merged_PXD005207A$Group <- paste0(Merged_PXD005207A$pipeline.x,"_",Merged_PXD005207A$pipeline.y,"_",Merged_PXD005207A$pipeline)
Merged_PXD005207A$Group <- gsub('_NA', '', Merged_PXD005207A$Group)
Merged_PXD005207A$Group <- gsub('NA_', '', Merged_PXD005207A$Group)
Merged_PXD009157A$Group <- paste0(Merged_PXD009157A$pipeline.x,"_",Merged_PXD009157A$pipeline.y,"_",Merged_PXD009157A$pipeline)
Merged_PXD009157A$Group <- gsub('_NA', '', Merged_PXD009157A$Group)
Merged_PXD009157A$Group <- gsub('NA_', '', Merged_PXD009157A$Group)
Merged_PXD009465A$Group <- paste0(Merged_PXD009465A$pipeline.x,"_",Merged_PXD009465A$pipeline.y,"_",Merged_PXD009465A$pipeline)
Merged_PXD009465A$Group <- gsub('_NA', '', Merged_PXD009465A$Group)
Merged_PXD009465A$Group <- gsub('NA_', '', Merged_PXD009465A$Group)
Merged_PXD026474A$Group <- paste0(Merged_PXD026474A$pipeline.x,"_",Merged_PXD026474A$pipeline.y,"_",Merged_PXD026474A$pipeline)
Merged_PXD026474A$Group <- gsub('_NA', '', Merged_PXD026474A$Group)
Merged_PXD026474A$Group <- gsub('NA_', '', Merged_PXD026474A$Group)
tab1(Merged_PXD001684A$Group)
tab1(Merged_PXD002266A$Group)
tab1(Merged_PXD005207A$Group)
tab1(Merged_PXD009157A$Group)
tab1(Merged_PXD009465A$Group)
tab1(Merged_PXD026474A$Group)
PXD026474A_TPP <- rbind.data.frame(PXD026474A_1_TPP,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP$Spectrum))
# Supp Table 2 - Comparing PSM + Number of phosphorylations across data sets #
##############################################################################
#> [conflicted] Will prefer dplyr::filter over any other package
suppressPackageStartupMessages(library("tidyverse"))
library(dplyr)
library(stringr)
library(useful)
library(MASS)
library(reshape2)
library(epiDisplay)
PXD001684A_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD001684.csv')
PXD002266A_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD002266.csv')
PXD005207A_1_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_Plasmo.csv')
PXD005207A_2_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_Plfalci.csv')
PXD005207A_3_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigMix.csv')
PXD005207A_4_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR1.csv')
PXD005207A_5_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR2.csv')
PXD005207A_6_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR3.csv')
PXD005207A_7_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR4.csv')
PXD005207A_8_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_SigR5.csv')
PXD005207A_9_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_StageR1.csv')
PXD005207A_10_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_StageR4.csv')
PXD005207A_11_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD005207_StageR5.csv')
PXD009157A_1_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD009157_1.csv')
PXD009157A_2_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD009157_2.csv')
PXD009465A_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD009465.csv')
PXD026474A_1_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD026474_KO.csv')
PXD026474A_2_TPP <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/TPP/Plasmodium/TPP_PXD026474_WT.csv')
PXD001684A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD001684_A_PSMSITE.csv')
PXD002266A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD002266_A_PSMSITE.csv')
PXD005207A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD005207_A_PSMSITE.csv')
PXD009157A_1_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD009157_1_A_PSMSITE.csv')
PXD009157A_2_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD009157_2_A_PSMSITE.csv')
PXD009465A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD009465_A_PSMSITE.csv')
PXD026474A_MQ <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/MQ/Plasmodium/MQ_PXD026474_A_PSMSITE.csv')
PXD001684A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD001684A_PSMSITE.csv')
PXD002266A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD002266A_PSMSITE.csv')
PXD005207A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD005207A_PSMSITE.csv')
PXD009157A_1_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD009157A_1_PSMSITE.csv')
PXD009157A_2_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD009157A_2_PSMSITE.csv')
PXD009465A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD009465A_PSMSITE.csv')
PXD026474A_PD <- read.csv(file = 'D:/Pipeline comparisons/Writing/Data/PD/Plasmodium/PD_PXD026474A_PSMSITE.csv')
PXD001684A_TPP$Seq_nPhospho <- paste0(PXD001684A_TPP$Peptide,"_",str_count(PXD001684A_TPP$Peptide_mod,"Phospho"))
PXD002266A_TPP$Seq_nPhospho <- paste0(PXD002266A_TPP$Peptide,"_",str_count(PXD002266A_TPP$Peptide_mod,"Phospho"))
PXD005207A_1_TPP$Seq_nPhospho <- paste0(PXD005207A_1_TPP$Peptide,"_",str_count(PXD005207A_1_TPP$Peptide_mod,"Phospho"))
PXD005207A_2_TPP$Seq_nPhospho <- paste0(PXD005207A_2_TPP$Peptide,"_",str_count(PXD005207A_2_TPP$Peptide_mod,"Phospho"))
PXD005207A_3_TPP$Seq_nPhospho <- paste0(PXD005207A_3_TPP$Peptide,"_",str_count(PXD005207A_3_TPP$Peptide_mod,"Phospho"))
PXD005207A_4_TPP$Seq_nPhospho <- paste0(PXD005207A_4_TPP$Peptide,"_",str_count(PXD005207A_4_TPP$Peptide_mod,"Phospho"))
PXD005207A_5_TPP$Seq_nPhospho <- paste0(PXD005207A_5_TPP$Peptide,"_",str_count(PXD005207A_5_TPP$Peptide_mod,"Phospho"))
PXD005207A_6_TPP$Seq_nPhospho <- paste0(PXD005207A_6_TPP$Peptide,"_",str_count(PXD005207A_6_TPP$Peptide_mod,"Phospho"))
PXD005207A_7_TPP$Seq_nPhospho <- paste0(PXD005207A_7_TPP$Peptide,"_",str_count(PXD005207A_7_TPP$Peptide_mod,"Phospho"))
PXD005207A_8_TPP$Seq_nPhospho <- paste0(PXD005207A_8_TPP$Peptide,"_",str_count(PXD005207A_8_TPP$Peptide_mod,"Phospho"))
PXD005207A_9_TPP$Seq_nPhospho <- paste0(PXD005207A_9_TPP$Peptide,"_",str_count(PXD005207A_9_TPP$Peptide_mod,"Phospho"))
PXD005207A_10_TPP$Seq_nPhospho <- paste0(PXD005207A_10_TPP$Peptide,"_",str_count(PXD005207A_10_TPP$Peptide_mod,"Phospho"))
PXD005207A_11_TPP$Seq_nPhospho <- paste0(PXD005207A_11_TPP$Peptide,"_",str_count(PXD005207A_11_TPP$Peptide_mod,"Phospho"))
PXD009157A_1_TPP$Seq_nPhospho <- paste0(PXD009157A_1_TPP$Peptide,"_",str_count(PXD009157A_1_TPP$Peptide_mod,"Phospho"))
PXD009157A_2_TPP$Seq_nPhospho <- paste0(PXD009157A_2_TPP$Peptide,"_",str_count(PXD009157A_2_TPP$Peptide_mod,"Phospho"))
PXD009465A_TPP$Seq_nPhospho <- paste0(PXD009465A_TPP$Peptide,"_",str_count(PXD009465A_TPP$Peptide_mod,"Phospho"))
PXD026474A_1_TPP$Seq_nPhospho <- paste0(PXD026474A_1_TPP$Peptide,"_",str_count(PXD026474A_1_TPP$Peptide_mod,"Phospho"))
PXD026474A_2_TPP$Seq_nPhospho <- paste0(PXD026474A_2_TPP$Peptide,"_",str_count(PXD026474A_2_TPP$Peptide_mod,"Phospho"))
PXD001684A_PD$Seq_nPhospho <- paste0(PXD001684A_PD$Sequence,"_",PXD001684A_PD$n_Phos)
PXD002266A_PD$Seq_nPhospho <- paste0(PXD002266A_PD$Sequence,"_",PXD002266A_PD$n_Phos)
PXD005207A_PD$Seq_nPhospho <- paste0(PXD005207A_PD$Sequence,"_",PXD005207A_PD$n_Phos)
PXD009157A_1_PD$Seq_nPhospho <- paste0(PXD009157A_1_PD$Sequence,"_",PXD009157A_1_PD$n_Phos)
PXD009157A_2_PD$Seq_nPhospho <- paste0(PXD009157A_2_PD$Sequence,"_",PXD009157A_2_PD$n_Phos)
PXD009465A_PD$Seq_nPhospho <- paste0(PXD009465A_PD$Sequence,"_",PXD009465A_PD$n_Phos)
PXD026474A_PD$Seq_nPhospho <- paste0(PXD026474A_PD$Sequence,"_",PXD026474A_PD$n_Phos)
PXD001684A_MQ$Seq_nPhospho <- paste0(PXD001684A_MQ$Sequence,"_",str_count(PXD001684A_MQ$Modified.sequence,"Phospho"))
PXD002266A_MQ$Seq_nPhospho <- paste0(PXD002266A_MQ$Sequence,"_",str_count(PXD002266A_MQ$Modified.sequence,"Phospho"))
PXD005207A_MQ$Seq_nPhospho <- paste0(PXD005207A_MQ$Sequence,"_",str_count(PXD005207A_MQ$Modified.sequence,"Phospho"))
PXD009157A_1_MQ$Seq_nPhospho <- paste0(PXD009157A_1_MQ$Sequence,"_",str_count(PXD009157A_1_MQ$Modified.sequence,"Phospho"))
PXD009157A_2_MQ$Seq_nPhospho <- paste0(PXD009157A_2_MQ$Sequence,"_",str_count(PXD009157A_2_MQ$Modified.sequence,"Phospho"))
PXD009465A_MQ$Seq_nPhospho <- paste0(PXD009465A_MQ$Sequence,"_",str_count(PXD009465A_MQ$Modified.sequence,"Phospho"))
PXD026474A_MQ$Seq_nPhospho <- paste0(PXD026474A_MQ$Sequence,"_",str_count(PXD026474A_MQ$Modified.sequence,"Phospho"))
# PSM count at 1% FDR #
PXD001684A_TPP_PSM <- length(unique(PXD001684A_TPP$Spectrum))
PXD002266A_TPP_PSM <- length(unique(PXD002266A_TPP$Spectrum))
PXD005207A_TPP<- rbind.data.frame(PXD005207A_1_TPP,PXD005207A_2_TPP,PXD005207A_3_TPP,PXD005207A_4_TPP,PXD005207A_5_TPP,
PXD005207A_6_TPP,PXD005207A_7_TPP,PXD005207A_8_TPP,PXD005207A_9_TPP,PXD005207A_10_TPP,
PXD005207A_11_TPP)
PXD005207A_TPP_PSM <- length(unique(PXD005207A_TPP$Spectrum))
PXD009157A_TPP <- rbind.data.frame(PXD009157A_1_TPP,PXD009157A_2_TPP)
PXD009157A_TPP_PSM <- length(unique(PXD009157A_TPP$Spectrum))
PXD009465A_TPP_PSM <- length(unique(PXD009465A_TPP$Spectrum))
PXD026474A_TPP <- rbind.data.frame(PXD026474A_1_TPP,PXD026474A_2_TPP)
PXD026474A_TPP_PSM <- length(unique(PXD026474A_TPP$Spectrum))
PXD001684A_PD_PSM <- length(unique(paste0(PXD001684A_PD$File.ID,"_",PXD001684A_PD$First.Scan)))
PXD002266A_PD_PSM <- length(unique(paste0(PXD002266A_PD$File.ID,"_",PXD002266A_PD$First.Scan)))
PXD005207A_PD_PSM <- length(unique(paste0(PXD005207A_PD$File.ID,"_",PXD005207A_PD$First.Scan)))
PXD009157A_PD <- rbind.data.frame(PXD009157A_1_PD,PXD009157A_2_PD)
PXD009157A_PD_PSM <- length(unique(paste0(PXD009157A_PD$File.ID,"_",PXD009157A_PD$First.Scan)))
PXD009465A_PD_PSM <- length(unique(paste0(PXD009465A_PD$File.ID,"_",PXD009465A_PD$First.Scan)))
PXD026474A_PD_PSM <- length(unique(paste0(PXD026474A_PD$File.ID,"_",PXD026474A_PD$First.Scan)))
PXD001684A_MQ_PSM <- length(unique(paste0(PXD001684A_MQ$Spectrum,"_",PXD001684A_MQ$MS.MS.IDs)))
PXD002266A_MQ_PSM <- length(unique(paste0(PXD002266A_MQ$Spectrum,"_",PXD002266A_MQ$MS.MS.IDs)))
PXD005207A_MQ_PSM <- length(unique(paste0(PXD005207A_MQ$Spectrum,"_",PXD005207A_MQ$MS.MS.IDs)))
PXD009157A_MQ <- rbind.data.frame(PXD009157A_1_MQ,PXD009157A_2_MQ)
PXD009157A_MQ_PSM <- length(unique(paste0(PXD009157A_MQ$Spectrum,"_",PXD009157A_MQ$MS.MS.IDs)))
PXD009465A_MQ_PSM <- length(unique(paste0(PXD009465A_MQ$Spectrum,"_",PXD009465A_MQ$MS.MS.IDs)))
PXD026474A_MQ_PSM <- length(unique(paste0(PXD026474A_MQ$Spectrum,"_",PXD026474A_MQ$MS.MS.IDs)))
# Unique PSMs + nPhospho
Unique_PXD001684A_TPP <- cbind.data.frame(distinct(PXD001684A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD002266A_TPP <- cbind.data.frame(distinct(PXD002266A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD005207A_TPP <- cbind.data.frame(distinct(PXD005207A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD009157A_TPP <- cbind.data.frame(distinct(PXD009157A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD009465A_TPP <- cbind.data.frame(distinct(PXD009465A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD026474A_TPP <- cbind.data.frame(distinct(PXD026474A_TPP,Seq_nPhospho),pipeline="TPP")
Unique_PXD001684A_PD <- cbind.data.frame(distinct(PXD001684A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD002266A_PD <- cbind.data.frame(distinct(PXD002266A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD005207A_PD <- cbind.data.frame(distinct(PXD005207A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD009157A_PD <- cbind.data.frame(distinct(PXD009157A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD009465A_PD <- cbind.data.frame(distinct(PXD009465A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD026474A_PD <- cbind.data.frame(distinct(PXD026474A_PD,Seq_nPhospho),pipeline="PD")
Unique_PXD001684A_MQ <- cbind.data.frame(distinct(PXD001684A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD002266A_MQ <- cbind.data.frame(distinct(PXD002266A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD005207A_MQ <- cbind.data.frame(distinct(PXD005207A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD009157A_MQ <- cbind.data.frame(distinct(PXD009157A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD009465A_MQ <- cbind.data.frame(distinct(PXD009465A_MQ,Seq_nPhospho),pipeline="MQ")
Unique_PXD026474A_MQ <- cbind.data.frame(distinct(PXD026474A_MQ,Seq_nPhospho),pipeline="MQ")
# Merging data #
################
M1_PXD001684A <- merge(Unique_PXD001684A_TPP,Unique_PXD001684A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD001684A <- merge(M1_PXD001684A,Unique_PXD001684A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD002266A <- merge(Unique_PXD002266A_TPP,Unique_PXD002266A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD002266A <- merge(M1_PXD002266A,Unique_PXD002266A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD005207A <- merge(Unique_PXD005207A_TPP,Unique_PXD005207A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD005207A <- merge(M1_PXD005207A,Unique_PXD005207A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD009157A <- merge(Unique_PXD009157A_TPP,Unique_PXD009157A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD009157A <- merge(M1_PXD009157A,Unique_PXD009157A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD009465A <- merge(Unique_PXD009465A_TPP,Unique_PXD009465A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD009465A <- merge(M1_PXD009465A,Unique_PXD009465A_MQ, by="Seq_nPhospho", all = TRUE)
M1_PXD026474A <- merge(Unique_PXD026474A_TPP,Unique_PXD026474A_PD, by="Seq_nPhospho", all = TRUE)
Merged_PXD026474A <- merge(M1_PXD026474A,Unique_PXD026474A_MQ, by="Seq_nPhospho", all = TRUE)
Merged_PXD001684A$Group <- paste0(Merged_PXD001684A$pipeline.x,"_",Merged_PXD001684A$pipeline.y,"_",Merged_PXD001684A$pipeline)
Merged_PXD001684A$Group <- gsub('_NA', '', Merged_PXD001684A$Group)
Merged_PXD001684A$Group <- gsub('NA_', '', Merged_PXD001684A$Group)
Merged_PXD002266A$Group <- paste0(Merged_PXD002266A$pipeline.x,"_",Merged_PXD002266A$pipeline.y,"_",Merged_PXD002266A$pipeline)
Merged_PXD002266A$Group <- gsub('_NA', '', Merged_PXD002266A$Group)
Merged_PXD002266A$Group <- gsub('NA_', '', Merged_PXD002266A$Group)
Merged_PXD005207A$Group <- paste0(Merged_PXD005207A$pipeline.x,"_",Merged_PXD005207A$pipeline.y,"_",Merged_PXD005207A$pipeline)
Merged_PXD005207A$Group <- gsub('_NA', '', Merged_PXD005207A$Group)
Merged_PXD005207A$Group <- gsub('NA_', '', Merged_PXD005207A$Group)
Merged_PXD009157A$Group <- paste0(Merged_PXD009157A$pipeline.x,"_",Merged_PXD009157A$pipeline.y,"_",Merged_PXD009157A$pipeline)
Merged_PXD009157A$Group <- gsub('_NA', '', Merged_PXD009157A$Group)
Merged_PXD009157A$Group <- gsub('NA_', '', Merged_PXD009157A$Group)
Merged_PXD009465A$Group <- paste0(Merged_PXD009465A$pipeline.x,"_",Merged_PXD009465A$pipeline.y,"_",Merged_PXD009465A$pipeline)
Merged_PXD009465A$Group <- gsub('_NA', '', Merged_PXD009465A$Group)
Merged_PXD009465A$Group <- gsub('NA_', '', Merged_PXD009465A$Group)
Merged_PXD026474A$Group <- paste0(Merged_PXD026474A$pipeline.x,"_",Merged_PXD026474A$pipeline.y,"_",Merged_PXD026474A$pipeline)
Merged_PXD026474A$Group <- gsub('_NA', '', Merged_PXD026474A$Group)
Merged_PXD026474A$Group <- gsub('NA_', '', Merged_PXD026474A$Group)
tab1(Merged_PXD001684A$Group)
tab1(Merged_PXD002266A$Group)
tab1(Merged_PXD005207A$Group)
tab1(Merged_PXD009157A$Group)
tab1(Merged_PXD009465A$Group)
tab1(Merged_PXD026474A$Group)
PXD001684A_TPP_PSM
PXD002266A_TPP_PSM
PXD005207A_TPP_PSM
PXD009157A_TPP_PSM
PXD009465A_TPP_PSM
PXD026474A_TPP_PSM
PXD001684A_PD_PSM
PXD002266A_PD_PSM
PXD005207A_PD_PSM
PXD009157A_PD_PSM
PXD009465A_PD_PSM
PXD026474A_PD_PSM
PXD001684A_MQ_PSM
PXD002266A_MQ_PSM
PXD005207A_MQ_PSM
PXD009157A_MQ_PSM
PXD009465A_MQ_PSM
PXD026474A_MQ_PSM
