script2 {DIAlignR} | R Documentation |
Performs alignment using script1 output
script2( dataPath, outFile = "DIAlignR", params = paramsDIAlignR(), oswMerged = TRUE, runs = NULL, peps = NULL, refRun = NULL, applyFun = lapply )
dataPath |
(string) path to xics and osw directory. |
outFile |
(string) name of the output file. |
params |
(list) parameters are entered as list. Output of the |
oswMerged |
(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet. |
runs |
(string) names of xics file without extension. |
peps |
(integer) ids of peptides to be aligned. If NULL, align all peptides. |
refRun |
(string) reference for alignment. If no run is provided, m-score is used to select reference run. |
applyFun |
(function) value must be either lapply or BiocParallel::bplapply. |
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2021) + GPL-3 Date: 2021-02-20
params <- paramsDIAlignR() params[["context"]] <- "experiment-wide" dataPath <- system.file("extdata", package = "DIAlignR") BiocParallel::register(BiocParallel::MulticoreParam(workers = 4, progressbar = TRUE)) script1(dataPath, outFile = "testDIAlignR", params = params, applyFun = BiocParallel::bplapply) script2(dataPath, outFile = "testDIAlignR", params = params, applyFun = lapply) file.remove(file.path(dataPath, "testDIAlignR_script1.RData"))