Compute Counts for Venn Diagram

Description

This function is designed to compute counts for a Venn diagram. It is slightly different from vennCounts in the additional ability to compute counts for genes that are differentially expressed in the same direction.

Usage

vennCounts2(x, method = "same", fit = NULL, foldFilt = NULL)

Arguments

Details

The function vennCounts will return identical results except for the "same" method. This will only select those genes that both pass the criteria of decideTests as well as being differentially expressed in the same direction. Note that this is different from the "both" method, which simply requires that a given gene be differentially expressed in e.g., two different comparisons without any requirement that the direction be the same.

Value

A VennCounts object.

Author(s)

James W. MacDonald <jmacdon@u.washington.edu>

Examples

library("limma")
tstat <- matrix(rt(300,df=10),100,3)
tstat[1:33,] <- tstat[1:33,]+2
clas <- classifyTestsF(tstat,df=10,p.value=0.05)
a <- vennCounts2(clas)
print(a)
vennDiagram(a)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(affycoretools)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.




Attaching package: 'affycoretools'

The following object is masked from 'package:BiocGenerics':

    plotPCA

Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affycoretools/vennCounts2.Rd_%03d_medium.png", width=480, height=480)
> ### Name: vennCounts2
> ### Title: Compute Counts for Venn Diagram
> ### Aliases: vennCounts2
> ### Keywords: hplot manip
> 
> ### ** Examples
> 
> 
> library("limma")

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

> tstat <- matrix(rt(300,df=10),100,3)
> tstat[1:33,] <- tstat[1:33,]+2
> clas <- classifyTestsF(tstat,df=10,p.value=0.05)
> a <- vennCounts2(clas)
> print(a)
  Group 1 Group 2 Group 3 Counts
1       0       0       0     81
2       0       0       1      4
3       0       1       0      2
4       0       1       1      6
5       1       0       0      1
6       1       0       1      2
7       1       1       0      1
8       1       1       1      3
attr(,"class")
[1] "VennCounts"
> vennDiagram(a)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>