progTree1 {DIAlignR} | R Documentation |
Step 1 for progressive alignment
progTree1( dataPath, params, categ = NULL, outFile = "DIAlignR", oswMerged = TRUE, peps = NULL, runs = NULL, newickTree = NULL, applyFun = lapply )
dataPath |
(string) path to xics and osw directory. |
params |
(list) parameters are entered as list. Output of the |
categ |
(data-frame) contains the run names and their categories/batch id to keep them on the same branch of the tree. |
outFile |
(string) name of the output file. |
oswMerged |
(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet. |
peps |
(integer) ids of peptides to be aligned. If NULL, align all peptides. |
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. |
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2021) + GPL-3 Date: 2021-03-03