alignTargetedRuns2 {DIAlignR} | R Documentation |
Star alignment for few ids
alignTargetedRuns2( dataPath, outFile = "DIAlignR.tsv", params, ids = NULL, oswMerged = TRUE, runs = 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. |
applyFun |
(function) value must be either lapply or BiocParallel::bplapply. |
(None)
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2021) + GPL-3 Date: 2021-01-20
## Not run: ids <- as.integer(scan(file = "data/ids.txt")) params <- paramsDIAlignR() params[["maxFdrQuery"]] <- 1.0 params[["maxPeptideFdr"]] <- 1.0 params[["kernelLen"]] <- 11L params$globalAlignmentFdr <- 0.001 params[["batchSize"]] <- 1000L BiocParallel::register(BiocParallel::MulticoreParam(workers = 6, log = FALSE, threshold = "INFO", stop.on.error = TRUE)) alignTargetedRuns2(dataPath = ".", params = params, outFile = "star", ids = ids, applyFun = BiocParallel::bplapply) ## End(Not run)