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

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

Aligns an analyte from an experiment to the reference run

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,
  feature_alignment_map = NULL
)

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.
refIdx	(integer) index of the reference feature in df.
fileInfo	(data-frame) output of getRunNames.
XICs	(list of dataframes) fragment-ion chromatograms of the analytes for all runs.
XICs.ref	(list of dataframes) fragment-ion chromatograms of the analyte_chr from the reference run.
params	(list) parameters are entered as list. Output of the paramsDIAlignR function.
df	(dataframe) a collection of features related to the peptide
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.
feature_alignment_mapping	(data.table) contains experiment feature ids mapped to corresponding reference feature id per analyte. This is an output of getRefExpFeatureMap.

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, getRefExpFeatureMap

Examples

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

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