getIsoDiffReport: Compare isotope labeling reports

In yufree/x13cms: Untargeted isotope-based metabolomics

Compare isotope labeling reports

Description

This routine matches up label-enriched isotopologue groups from each biological condition and determines whether the labeling patterns in each group are different between the conditions. To print the list to a tab-delimited file, use printIsoListOutputs.

Usage

getIsoDiffReport(labelsData1, labelsData2, condition1, condition2, classes1, classes2, labeledSamples, varEq, singleSample)

Arguments

labelsData1	isoLabelReport for samples from conditions 1
labelsData2	isoLabelReport for samples from conditions 2
condition1	character variable labeling condition 1, e.g. "control"
condition2	character variable labeling condition 2, e.g. "perturb"
classes1	character vector designating whether each sample in labelsData1 is unlabeled or labeled
classes2	character vector designating whether each sample in labelsData2 is unlabeled or labeled
labeledSamples	character variable designating labeled samples (e.g. "C13")
varEq	Boolean indicating whether to assume that relative isotopologue intensities in each condition are drawn from distributions with equal variance. Defaults to FALSE.
singleSample	Boolean indicating whether only single samples were used to generate the labeling reports. Defaults to FALSE

Value

An isoDiffReport consisting of the following lists describing isotopologue groups:

condition1	m/z of all isotopologues in a group in samples from condition 1; empty if group is found to be enriched for label only in condition 2
condition2	m/z of all isotopologues in a group in samples from condition 2; empty if group is found to be enriched for label only in condition 1
rt1	Retention time of each isotopologue in condition 1
rt2	Retention time of each isotopologue in condition 2
relInts1U	Mean relative intensities of each isotopologue in the samples of condition 1 treated with unlabeled precursor
relInts1L	Mean relative intensities of each isotopologue in the samples of condition 1 treated with labeled precursor
relInts2U	Mean relative intensities of each isotopologue in the samples of condition 2 treated with unlabeled precursor
relInts2L	Mean relative intensities of each isotopologue in the samples of condition 2 treated with labeled precursor
p_value	p-values from Welch's t-tests comparing relative intensities of each isotopologue in labeled samples of condition 1 vs. those of condition 2
sdRelInts1L	std dev of relative intensity of each isotopologue peak in labeled samples of condition 1
sdRelInts2L	std dev of relative intensity of each isotopologue peak in labeled samples of condition 2
absInts1L	mean absolute ion intensity of each isotopologue peak in labeled samples of condition 1
absInts2L	mean absolute ion intensity of each isotopologue peak in labeled samples of condition 2

Author(s)

Xiaojing Huang

Examples

## Not run: 
## isoDiffReport = getIsoDiffReport(labelsControl, labelsPerturb, condition1 = "control", condition2 = "perturb", classesControl = c("C12", "C12", "C13", "C13"), classesPerturb = c("C12", "C12", "C13", "C13"), labeledSamples = "C13", varEq = FALSE)
##
## This command generates the isoDiffReport for the example given for \code{\link{getIsoLabelReport}}

yufree/x13cms documentation built on Feb. 7, 2024, 3:24 p.m.