perBatch: Aligns an analyte across runs

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

Aligns an analyte across runs

Description

For the ith analyte in multipeptide, this function aligns all runs to the reference run. The result is a dataframe that contains aligned features corresponding to the analyte across all runs.

Usage

perBatch(
  iBatch,
  peptides,
  multipeptide,
  refRuns,
  precursors,
  prec2chromIndex,
  fileInfo,
  mzPntrs,
  params,
  globalFits,
  RSE,
  applyFun = lapply,
  multiFeatureAlignmentMap = NULL
)

Arguments

peptides	(integer) vector of peptide IDs.
multipeptide	(list) contains multiple data-frames that are collection of features associated with analytes. This is an output of getMultipeptide.
refRuns	(data-frame) output of getRefRun. Must have two columsn : transition_group_id and run.
precursors	(data-frame) atleast two columns transition_group_id and transition_ids are required.
prec2chromIndex	(list) a list of dataframes having following columns: transition_group_id: it is PRECURSOR.ID from osw file. chromatogramIndex: index of chromatogram in mzML file.
fileInfo	(data-frame) output of getRunNames.
mzPntrs	(list) a list of mzRpwiz.
params	(list) parameters are entered as list. Output of the paramsDIAlignR function.
globalFits	(list) each element is either of class lm or loess. This is an output of getGlobalFits.
RSE	(list) Each element represents Residual Standard Error of corresponding fit in globalFits.
multiFeatureAlignmentMap	(list) contains multiple data-frames that are collection of experiment feature ids mapped to corresponding reference feature id per analyte. This is an output of getRefExpFeatureMap.
rownum	(integer) represnts the index of the multipepetide to be aligned.

Value

invisible NULL

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-07-26

See Also

alignTargetedRuns, alignToRef, getAlignedTimesFast, getMultipeptide

Examples

dataPath <- system.file("extdata", package = "DIAlignR")

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