inst/doc/PTXQC-Basic_Guide_for_R_users.R

In PTXQC: Quality Report Generation for MaxQuant and mzTab Results

## ----eval=FALSE---------------------------------------------------------------
# vignette("PTXQC-InputData", package = "PTXQC")

## ----eval=FALSE---------------------------------------------------------------
# require(PTXQC)
# 
# ## the next require() is needed to prevent a spurious error in certain R versions (might be a bug in R or a package)
# ## error message is:
# ##    Error in Scales$new : could not find function "loadMethod"
# require(methods)
# 
# ## specify a path to a MaxQuant txt folder
# ## Note: This folder needs to be complete (see 'vignette("PTXQC-InputData", package = "PTXQC")')
# if (1) {
#   ## we will use an example dataset from PRIDE (dataset 2 of the PTXQC publication)
#   local_zip = tempfile(fileext=".zip")
#   tryCatch({
#     download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", destfile = local_zip)
#   }, error = function(err) {
#     ## on Windows, one can get a 'cannot open URL' using the default method. So we try another
#     download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", destfile = local_zip, method= "internal")
# 
#   })
#   unzip(local_zip, exdir = tempdir()) ## extracts content
#   txt_folder = file.path(tempdir(), "txt_20min")
# } else {
#   ## if you have local MaxQuant output, just use it
#   txt_folder = "c:/Proteomics/MouseLiver/combined/txt"
# }
# 
# r = createReport(txt_folder)
# 
# cat(paste0("\nReport generated as '", r$report_file, "'\n\n"))
# 

## ----eval=FALSE---------------------------------------------------------------
# vignette("PTXQC-CustomizeReport", package = "PTXQC")

## ----eval=FALSE---------------------------------------------------------------
# require(PTXQC)
# require(yaml)
# 
# ## the next require() is needed to prevent a spurious error in certain R versions (might be a bug in R or a package)
# ## error message is:
# ##    Error in Scales$new : could not find function "loadMethod"
# require(methods)
# 
# ## specify a path to a MaxQuant txt folder
# ## Note: This folder can be incomplete, depending on your YAML config
# if (1) {
#   ## we will use an example dataset from PRIDE (dataset 2 of the PTXQC publication)
#   local_zip = tempfile(fileext=".zip")
#   download.file("ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip", destfile = local_zip)
#   unzip(local_zip, exdir = tempdir()) ## extracts content
#   txt_folder = file.path(tempdir(), "txt_20min")
# } else {
#   ## if you have local MaxQuant output, just use it
#   txt_folder = "c:/Proteomics/MouseLiver/combined/txt"
# }
# 
# ## use a YAML config inside the target directory if present
# fh_out = getReportFilenames(txt_folder)
# if (file.exists(fh_out$yaml_file))
# {
#   cat("\nUsing YAML config already present in target directory ...\n")
#   yaml_config = yaml.load_file(input = fh_out$yaml_file)
# } else {
#   cat("\nYAML config not found in folder '", txt_folder, "'. The first run of PTXQC will create one for you.", sep="")
#   yaml_config = list()
# }
# 
# r = createReport(txt_folder, mztab_file = NULL, yaml_obj = yaml_config)
# 
# cat(paste0("\nReport generated as '", r$report_file, "'\n\n"))
#