alignToRef: Aligns an analyte from an experiment to the reference run

In Roestlab/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

df contains unaligned features for an analyte across multiple runs. This function aligns eXp run to ref run and updates corresponding features.

Usage

alignToRef(
  eXp,
  ref,
  refIdx,
  fileInfo,
  XICs,
  XICs.ref,
  params,
  df,
  globalFits,
  RSE
)

Arguments

eXp	(string) name of the run to be aligned to reference run. Must be in the rownames of fileInfo.
ref	(string) name of the reference run. Must be in the rownames of fileInfo.
fileInfo	(data-frame) output of getRunNames.
params	(list) parameters are entered as list. Output of the paramsDIAlignR function.
df	(dataframe) a collection of features related to analyte_chr.
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.
analyte_chr	(string) Precursor ID of the requested analyte.
XICs.ref.s	(list of dataframes) Smoothed fragment-ion chromatograms of the analyte_chr from the reference run.

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, perBatch, setAlignmentRank, getMultipeptide

Examples

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

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.