getChildFeature: 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

getChildFeature(XICs, alignedVec, df.ref, df.eXp, i.ref, i.eXp, params)

Arguments

XICs	(list of data-frames) extracted ion chromatograms from the child run.
alignedVec	(data-frame) aligned parent time-vectors. Must have five columns
df.ref	(data-frame) contains reference-run features to be transformed. It has a format of getFeatures output.
df.eXp	(data-frame) contains experiment-run 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

trfrParentFeature, getNodeRun

Examples

data(masterXICs_DIAlignR, package="DIAlignR")
newXICs <- masterXICs_DIAlignR
params <- paramsDIAlignR()
dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- DIAlignR::getRunNames(dataPath = dataPath)
features <- getFeatures(fileInfo, maxFdrQuery = 1.00, runType = "DIA_Proteomics")
df.ref <- features$run1[features$run1$transition_group_id == 4618L, ]
df.eXp <- features$run2[features$run2$transition_group_id == 4618L, ]
## Not run: 
getChildFeature(newXICs[[1]], newXICs[[2]], df.ref, df.eXp, params)

## End(Not run)

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