getAlignedFigs: Plot aligned XICs group for a specific peptide.

Description Usage Arguments Value Author(s) Examples

Description

AlignObj is the output from getAlignObjs fucntion. This function prepares ggplot objects from AlignObj.

Usage

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getAlignedFigs(
  AlignObj,
  XICs.ref,
  XICs.eXp,
  refPeakLabel,
  annotatePeak = FALSE
)

Arguments

AlignObj

(S4 object)

XICs.ref

(list) List of extracted ion chromatograms (dataframe) from reference run. The dataframe has two columns: first column is for time and second column indicates intensity.

XICs.eXp

(list) List of extracted ion chromatograms (dataframe) from experiment run.The dataframe has two columns: first column is for time and second column indicates intensity.

refPeakLabel

(numeric vector) It contains peak apex, left width and right width.

annotatePeak

(logical) TRUE: Peak boundaries and apex will be highlighted.

Value

A plot to the current device.

Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-13

Examples

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dataPath <- system.file("extdata", package = "DIAlignR")
runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt",
 "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt")
AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath)
AlignObj <- AlignObjOutput[[2]][["4618"]][[1]][["AlignObj"]]
XICs.ref <- AlignObjOutput[[2]][["4618"]][[1]][["ref"]]
XICs.eXp <- AlignObjOutput[[2]][["4618"]][[1]][["eXp"]]
refPeakLabel <- AlignObjOutput[[2]][["4618"]][[1]][["peak"]]
## Not run: 
getAlignedFigs(AlignObj, XICs.ref, XICs.eXp, refPeakLabel)

## End(Not run)

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