In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

This 2D-TPP analysis was executed on r format(Sys.time(), "%a %b %d %X %Y") on machine r Sys.info()["nodename"] with the following parameters:

str_break <- function(x, width = 80L) {
   n <- nchar(x)
   if (n <= width) {
      return(x)
   }
   n1 <- seq(1L, n, by = width)
   n2 <- seq(width, n, by = width)
   if (n %% width != 0) {
      n2 = c(n2, n)
   }

   substring(x, n1, n2)
}

Analyzed experiments

if ("Path" %in% colnames(configTable)){
  tab1 <- configTable %>%
  select(Compound, Experiment, Temperature, Path)
  kable(tab1)
}else {
    tab1 <- configTable %>%
  select(Compound, Experiment, Temperature)
  kable(tab1)
}


tab2 <- melt(extractConc(configTable))
# find respective reference columns
tab2$ref <- sapply(rownames(tab2), function(rn){
  ref <- unique(configTable$RefCol[which(configTable[[rn]]!="-")])
  return(ref)
})
colnames(tab2) <- c("Concentration [uM]", "Reference label")
kable(tab2, row.names=TRUE)

Configuration file

print(configFile)

User defined settings

if (is.null(fcStr)){
  fcStr <- "none"
}
if (is.null(fcStrUpdated)){
  fcStrUpdated <- "none"
}
if (is.null(addCol)){
  addCol <- "none"
}


param <- c("Protein identifier", "Fold change suffix", 
           "Updated Fold change suffix (after normalization)", "Intensity value suffix", 
           "Median normalization", "Added columns", "R2 cutoff", "Fold change cutoff",
           "Slope bounds", "Chosen methods for analysis", "TR reference data set")
variab <- c(idVar, fcStr, fcStrUpdated, intensityStr, normalize, addCol, r2Cutoff, fcCutoff, 
            paste(as.character(slopeBounds), collapse=","), paste(methods, sep=" "),  trRef)

tab <- data.frame(param, variab)
colnames(tab) <- c("Parameter", "Setting")
kable(tab)

Applied R version

rver <- sessionInfo()[["R.version"]][["version.string"]]
print(rver)

Applied R packages

pnames <- loadedNamespaces()
pvers <- unlist(lapply(pnames, function(pn) as.character(packageVersion(pn))))
ptab <- data.frame(pnames, pvers)
colnames(ptab) <- c("Package", "Version")
kable(ptab)