progAlignRuns2 {DIAlignR} | R Documentation |
Progressive alignment for few ids
progAlignRuns2( dataPath, params, outFile = "DIAlignR.tsv", ropenms, ids = NULL, oswMerged = TRUE, runs = NULL, newickTree = NULL, applyFun = lapply )
dataPath |
(string) path to xics and osw directory. |
params |
(list) parameters are entered as list. Output of the |
outFile |
(string) name of the output file. |
ropenms |
(pyopenms module) get this python module through |
oswMerged |
(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet. |
runs |
(string) names of xics file without extension. |
newickTree |
(string) guidance tree in newick format. Look up |
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"]] <- 11 params$batchSize <- 10000L params$globalAlignmentFdr <- 0.001 BiocParallel::register(BiocParallel::MulticoreParam(workers = 6, log = FALSE, threshold = "INFO", stop.on.error = TRUE)) ropenms <- get_ropenms(condaEnv = "TricEnvr") progAlignRuns2(dataPath = ".", params = params, outFile = "prog", ropenms = ropenms, ids = ids, applyFun = BiocParallel::bplapply) ## End(Not run)