find.Overlapping.mzs: find.Overlapping.mzs

In yufree/xMSanalyzer: xMSanalyzer: R package for data analysis, comparison, and annotation of metabolomics data.

Description

This function matches features between two datasets using the following user defined criteria: 1) Maximum m/z difference (+/-) ppm 2) Maximum retention time difference in seconds

Usage

find.Overlapping.mzs(dataA, dataB, mz.thresh = 10, time.thresh = NA, alignment.tool = NA)

Arguments

dataA	apLCMS or XCMS feature table for dataset A
dataB	apLCMS or XCMS feature table for dataset B
mz.thresh	Maximum m/z difference (+/-) ppm. eg: 10
time.thresh	Maximum retention time difference (+/-) secs. eg: 300
alignment.tool	Name of the feature alignment tool eg: "apLCMS" or "XCMS" or "NA" Use "NA" if the input matrix includes only m/z or both m/z and retnetion time values.

Details

The find.Overlapping.mzs function operates on two sets of feature lists with m/z and retention times for each feature, denoted by L1 and L2, and iterates over all m/z values in L1 to find those that are within a user defined m/z (ppm) and retention time (sec) threshold in L2. Optionally, the user can match features based on only the m/z values by setting time.thresh=NA. The find.Unique.mzs function uses a similar algorithm to find unique features that are not within a user defined mass and retention time threshold level.

Value

Matrix of overlapping features with columns: index.data.A: index of overlapping m/z in dataset A mz.data.A: m/z in dataset A time.data.A: retention time in dataset A index.data.B: index of overlapping m/z in dataset B mz.data.B: m/z in dataset B time.data.B: retention time in dataset B

Author(s)

Karan Uppal <[e-mail]>

See Also

apLCMS.align, XCMS.align, find.Unique.mzs, getVenn

yufree/xMSanalyzer documentation built on May 4, 2019, 6:35 p.m.