mstAlignRuns: Peptide quantification through MST alignment

In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Peptide quantification through MST alignment

Description

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 guide-tree is built using mst which can also be provided with mstNet parameter. As we traverse from the start node to the other nodes, runs are aligned pairwise.

Usage

mstAlignRuns(
  dataPath,
  outFile = "DIAlignR",
  params = paramsDIAlignR(),
  oswMerged = TRUE,
  scoreFile = NULL,
  runs = NULL,
  peps = NULL,
  mstNet = NULL,
  applyFun = lapply
)

Arguments

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 paramsDIAlignR function.
oswMerged	(logical) TRUE if merged file from pyprophet is used.
scoreFile	(string) path to the peptide score file, needed when oswMerged is FALSE.
runs	(string) names of xics file without extension.
peps	(integer) ids of peptides to be aligned. If NULL, align all peptides.
mstNet	(matrix) array of tree-edges. Look up getMST.
applyFun	(function) value must be either lapply or BiocParallel::bplapply.

Value

(None)

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-05-15

See Also

alignTargetedRuns, progAlignRuns, getMST

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
params <- paramsDIAlignR()
params[["context"]] <- "experiment-wide"
mstAlignRuns(dataPath, params = params, outFile = "DIAlignR")
## Not run: 
y <- strsplit("run0 run1\nrun2 run2", split = '\n')[[1]]
y <- cbind(A = strsplit(y[1], " ")[[1]], B = strsplit(y[2], " ")[[1]])
plot(igraph::graph_from_edgelist(y, directed = FALSE))

## End(Not run)

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.