mstAlignRuns {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 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.
mstAlignRuns( dataPath, params, outFile = "DIAlignR", oswMerged = TRUE, runs = NULL, peps = NULL, mstNet = 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. |
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. |
mstNet |
(matrix) array of tree-edges. 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: 2021-05-15
alignTargetedRuns, progAlignRuns, getMST
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)