progAlignRuns {DIAlignR} | R Documentation |
This function expects osw and xics directories at dataPath. It first reads osw files and fetches chromatogram indices for each analyte. To perform alignment, first a crude guide-tree is built which can also be provided with newickTree parameter. As we traverse from the leaf-nodes to the root node, runs are aligned pairwise. The root node is named master1 that has average of all fragment ion chromatograms and identified peak-groups. These features are propagated back to leaf nodes and finally aligned features are written in the output file.
progAlignRuns( dataPath, params, outFile = "DIAlignR", ropenms = NULL, oswMerged = TRUE, runs = NULL, peps = 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. |
peps |
(integer) ids of peptides to be aligned. If NULL, align all peptides. |
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 (2020) + GPL-3 Date: 2020-07-10
dataPath <- system.file("extdata", package = "DIAlignR") params <- paramsDIAlignR() params[["context"]] <- "experiment-wide" ## Not run: ropenms <- get_ropenms(condaEnv = "envName") progAlignRuns(dataPath, params = params, outFile = "test3", ropenms = ropenms) # Removing aligned vectors file.remove(list.files(dataPath, pattern = "*_av.rds", full.names = TRUE)) # Removing temporarily created master chromatograms file.remove(list.files(file.path(dataPath, "xics"), pattern = "^master[A-Za-z0-9]+\\.chrom\\.sqMass$", full.names = TRUE)) file.remove(file.path(dataPath, "test3.temp.RData")) file.remove(file.path(dataPath, "master.merged.osw")) ## End(Not run)