getVennmultiple: getVennmultiple

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

Description

This utility calls the find.Overlapping.mzs function and generates a Venn diagram showing the extent of overlap between three datasets.

Usage

getVennmultiple(dataA, name_a, dataB, name_b, dataC, name_c, mz.thresh = 10, 
    time.thresh = 30, alignment.tool, xMSanalyzer.outloc, use.unique.mz = FALSE, 
    plotvenn = TRUE)

Arguments

dataA	apLCMS or XCMS feature table for dataset A as a data frame.
name_a	Name of dataset A (eg: "SetA").
dataB	apLCMS or XCMS feature table for dataset B as a data frame.
name_b	Name of dataset B (eg: "SetB")
dataC	apLCMS or XCMS feature table for dataset B as a data frame.
name_c	Name of dataset C (eg: "SetC")
mz.thresh	+/- ppm threshold for m/z matching. eg: 10
time.thresh	Maximum retention time difference (+/-) secs. eg: 30
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.
xMSanalyzer.outloc	xMSanalyzer output location, eg: "C:/experiment1/xMSanalyzeroutput/
use.unique.mz	If "TRUE", the function first finds unique features within each set
plotvenn	If "TRUE", the function plots the venn diagram.

Value

A list is returned.

uniqueA	Features that are unique in dataset A
uniqueB	Features that are unique in dataset B
uniqueC	Features that are unique in dataset C
common	Features that are common
vennCounts	Output of vennCounts function in limma package

Note

Only the unqiue m/zs within each dataset are used to generate Venn diagram.

Author(s)

Karan Uppal <[e-mail]>

References

http://rss.acs.unt.edu/Rdoc/library/limma/html/venn.html

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