Description Usage Arguments Value Note Author(s) References
This utility calls the find.Overlapping.mzs function and generates a Venn diagram showing the extent of overlap between three datasets.
1 2 3 | 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)
|
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. |
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 |
Only the unqiue m/zs within each dataset are used to generate Venn diagram.
Karan Uppal <kuppal2@emory.edu>
http://rss.acs.unt.edu/Rdoc/library/limma/html/venn.html
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