trfrParentFeature: Transform features to child time-domain

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

Description

This function transforms the peaks' times to child run's time-domain. The feature intensity is calculated with appropriate method stated in params. Internal missing values are not allowed in timeParent.

Usage

trfrParentFeature(XICs, timeParent, df, i, params)

Arguments

XICs	(list of data-frames) extracted ion chromatograms from the child run.
timeParent	(data-frame) has two columns: tAligned and alignedChildTime. tAligned is time vector from one of the parent run.
df	(data-frame) contains features to be transformed. It has a format of getFeatures output.
params	(list) parameters are entered as list. Output of the paramsDIAlignR function.

Value

(data-frame) this has a format of getFeatures output.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2020) + GPL-3 Date: 2020-07-17

See Also

getChildFeature

Examples

data(masterXICs_DIAlignR, package="DIAlignR")
newXICs <- masterXICs_DIAlignR
timeParent <- newXICs[[2]][, c("tAligned.ref", "alignedChildTime")]
colnames(timeParent) <- c("tAligned", "alignedChildTime")
params <- paramsDIAlignR()
dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- DIAlignR::getRunNames(dataPath = dataPath)
features <- getFeatures(fileInfo, maxFdrQuery = 1.00, runType = "DIA_Proteomics")
df <- features$run1[features$run1$transition_group_id == 4618L, ]
## Not run: 
trfrParentFeature(newXICs[[1]], timeParent, df, params)

## End(Not run)

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