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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.
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