getIsoDiffReport: Compare isotope labeling reports

Description Usage Arguments Value Author(s) Examples

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

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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

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## 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 May 4, 2019, 6:35 p.m.