PGexport: PGexport results

In cpanse/NestLink: NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles

PGexport results

Description

PGexport results

Author(s)

Pascal Egloff [e-mail]

Source

https://fgcz-bfabric.uzh.ch

• Workunit : 158716 - QEXACTIVEHF_1 20170919_16_62465_nl5idx1-3_6titratecoli.raw 20170919_05_62465_nl5idx1-3_6titratecoli.raw

• Workunit : 158717 - QEXACTIVEHF_1 20170919_14_62466_nl5idx1-3_7titratesmeg.raw 20170919_09_62466_nl5idx1-3_7titratesmeg.raw

Examples

# filename <- system.file(
#  "extdata/PGexport2_normalizedAgainstSBstandards_Peptides.csv",
#  package = "NestLink")
library(ExperimentHub)
eh <- ExperimentHub()
filename <- query(eh,
  c("NestLink", "PGexport2_normalizedAgainstSBstandards_Peptides.csv"))[[1]]
P <- read.csv(filename, header = TRUE, sep=';')
P <- P[P$Modifications == '', ]
P <- P[,c('Accession', 'Sequence',
"X20170919_05_62465_nl5idx1.3_6titratecoli",
"X20170919_16_62465_nl5idx1.3_6titratecoli",
"X20170919_09_62466_nl5idx1.3_7titratesmeg",
"X20170919_14_62466_nl5idx1.3_7titratesmeg")]
names(P)<-c('Accession','Sequence','coli1', 'coli2', 'smeg1', 'smeg2')
P<- P[grep("^P[0-9][A-Z][0-9]", P$Accession), ]

P$FCset_ng <- NA
P$FCset_ng[P$Accession %in% c('P1A4', 'P1B4', 'P1C4',
  'P1D4', 'P1E4', 'P1F4')] <- 92
P$FCset_ng[P$Accession %in% c('P1A5', 'P1B5', 'P1C5',
  'P1D5', 'P1G4', 'P1H4')] <- 295
P$FCset_ng[P$Accession %in% c('P1A6', 'P1B6', 'P1E5',
  'P1F5', 'P1G5', 'P1H5')] <- 943
P$FCset_ng[P$Accession %in% c('P1C6', 'P1D6', 'P1E6',
  'P1F6', 'P1G6', 'P1H6')] <- 3017

 P$coli1 <- (log(P$coli1,2) - mean(log(P$coli1,2))) / sd(log(P$coli1,2))
 P$coli2 <- (log(P$coli2,2) - mean(log(P$coli2,2))) / sd(log(P$coli2,2))
 P$smeg1 <- (log(P$smeg1,2) - mean(log(P$smeg1,2))) / sd(log(P$smeg1,2))
 P$smeg2 <- (log(P$smeg2,2) - mean(log(P$smeg2,2))) / sd(log(P$smeg2,2))

  O <- P
  b <- boxplot(df<-cbind(P$coli1 - P$coli2, P$coli1 - P$smeg1,
  P$coli1 - P$smeg2,P$coli2 - P$smeg1, P$coli2 - P$smeg2,
  P$smeg1 - P$smeg2),
   ylab='normalized log2ratios', ylim = c(-1,1), axes=FALSE,
    main=paste("ConcGr = all"))
axis(1, 1:6, c('coli[12]', 'coli1-smeg1', 'coli1-smeg2', 'coli2-smeg1',
'coli2- smeg2','smeg[12]'))
abline(h=0, col='red')
box()
axis(2)
axis(3, 1:6, b$n)
outliers.idx <- sapply(1:length(b$group), function(i){
  q <- df[, b$group[i]] == b$out[i];
  text(b$group[i], b$out[i], P[q, 2], pos=4, cex=0.4);
   text(b$group[i], b$out[i], P[q, 1], pos=2, cex=0.4);
   which(q)}
   )

cpanse/NestLink documentation built on May 16, 2022, 2:33 a.m.