miniDiffReport: Get XCMS-style diffReport from X13CMS data.

In yufree/x13cms: Untargeted isotope-based metabolomics

Get XCMS-style diffReport from X13CMS data.

Description

Generates conventional XCMS-like diff report comparing peaks between two sample classes, e.g. "control", and "treatment" from an xcmsSet object configured for X13CMS (i.e. one in which the sample classes have to be demarcated as unlabeled and labeled)

Usage

miniDiffReport(xcmsSet, class1sampNames, class2sampNames, varEq = FALSE, intChoice)

Arguments

xcmsSet	XCMS object
class1sampNames	The subset of rownames(xcmsSet@phenoData) corresponding to names of the unlabeled samples of class 1 (e.g. "control").
class2sampNames	The subset of rownames(xcmsSet@phenoData) corresponding to names of the unlabeled samples of class 2 (e.g. "perturb").
varEq	Boolean indicating whether to assume that absolute ion intensities of each peak in both sample classes are drawn from distributions with equal variance. Defaults to FALSE.
intChoice	one of "maxo", "into", or "intb"–the choice of which peak intensity measurement to use from the XCMS object.

Value

A dataframe whose rows correspond to peak groups identified in the xcmsSet object and whose columns are: - pvalue: p-value of Welch's t-test comparing absolute intensities of the peak in the two conditions - foldChange: change in mean peak intensity in condition 2 compared to conditions 1 - mzmed: median m/z of peak - rtmed: median retention time of peak - means1: mean peak intensity in condition 1 - means2: mean peak intensity in condition 2 - peakIntensities1: all peak intensities in the group in condition 1 - peakIntensities2: all peak intensities in the group in condition 2

Author(s)

Xiaojing Huang

Examples

## Not run:

## diffReport = miniDiffReport(xcmsSet, class1sampNames, class2sampNames, varEq = FALSE, intChoice = "intb") 

## From the example given in getIsoLabelReport(), the variables class1sampNames and class2sampNames would be c("control_unlabeled1", "control_unlabeled2"), and c("perturb_unlabeled1", "perturb_unlabeled2"), respectively.

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