getVenn: getVenn

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 two datasets.

Usage

getVenn(dataA, name_a, dataB, name_b, 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 A (eg: "SetB")
mz.thresh	+/- ppm mass tolerance for m/z matching
time.thresh	Maximum retention time difference (+/-) secs. eg: 30
alignment.tool	"apLCMS" or "XCMS" or "NA". If NA is specified then the first two columns are treated as m/z and retention time, respectively.
xMSanalyzer.outloc	Output folder, 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.

Details

This utility calls the find.Overlapping.mzs and find.Unique.mzs functions and generates a Venn diagram showing the extent of overlap between datasets (up to three).

Value

A list is returned.

common	Row numbers, m/zs, delta retention times of features that are common between the two datasets.
commonA	Overlapping features in dataset A
uniqueA	Features that are unique in dataset A
commonB	Overlapping features in dataset B
uniqueB	Features that are unique in dataset B
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.