This vignette serves as a quickstart guide for R users to create a report from within R using PTXQC.
Target Audience: R users
Reports can be generated using the default configuration of PTXQC. See
vignette("PTXQC-InputData", package = "PTXQC")
how a txt folder should look like.
This is the most simple invokation of PTXQC::createReport().
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"))
The report can be customized via a YAML configuration file. For details, see
vignette("PTXQC-CustomizeReport", package = "PTXQC")
After editing the YAML configuration to your needs, run the code below.
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"))
That’s it.