overlapProtTrans.Specific: Compute test of significance and draw venn diagram of the...

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

Compute test of significance and draw venn diagram of the observed overlap between the two data.frames.

Description

Compute test of significance and draw venn diagram of the observed overlap between the two data.frames.

Usage

overlapProtTrans.Specific(DF1, DF2, cond1, cond2, ratio = 1,
  common = TRUE, fig = TRUE, out, threshold = 1, thresholdDF1 = 0,
  categories = c("DF1", "DF2"), Col = c("coral4", "darkorchid1"),
  report = "", verbose = TRUE)

Arguments

DF1	numeric data.frame of the first study to compare
DF2	numeric data.frame of the second study to compare
cond1	character string, column name of the first data.frame being considered for the comparison
cond2	character string, column name of the second data.frame that being considered for the comparison
ratio	integer. Default: 1. Possible multiplier to apply to the first data.frame genes number to get the second data.frame genes number to consider for the comparison
common	boolean. Default: TRUE. Whether the two data.frames should comprise only the same genes for the comparison
fig	boolean. Default: TRUE. Whether the figure should also be printed directly
out	character string. "percent" or "pvalue"
threshold	numeric. Default: 1. Minimal expression for DF2 to be considered for the comparison
thresholdDF1	numeric. Default:0. Minimal expression for DF1 to be considered for the comparison
categories	character string vector of two. default: c('DF1','DF2'). Allows to give the name of the studies.
Col	numerical vectors of two. Default: "c('coral4','darkorchid1')" Colours for the venn diagram
report	character string. Default: ”. When report='html' use cat.html instead of print
verbose	boolean. Default: TRUE

Value

significance test and venn diagram

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.