Description
dGSEAwrite is supposed to write out enrichment results.
Usage
dGSEAwrite(eTerm, which_content = c("gadjp", "adjp", "pvalue", "FWER", "FDR", "qvalue",
"nES", "ES"), which_score = c("gadjp", "adjp", "FWER", "FDR", "qvalue", "nES"),
cutoff = 0.1, filename = NULL, keep.significance = T)
Arguments
- eTerm
- an object of class "eTerm"
- which_content
- the content will be written out. It includes two
categories: i) based on "adjp" for adjusted p value, "gadjp" for
globally adjusted p value, "pvalue" for p value, "FWER" for family-wise
error rate, "FDR" for false discovery rate, "qvalue" for q value; ii)
based on "ES" for enrichment score, "nES" for normalised enrichment
score. For the former, the content is : first -1*log10-transformed, and
then multiplied by -1 if nES is negative.
- which_score
- which statistics/score will be used for declaring
the significance. It can be "adjp" for adjusted p value, "gadjp" for
globally adjusted p value, "FWER" for family-wise error rate, "FDR" for
false discovery rate, "qvalue" for q value
- cutoff
- a cutoff to declare the signficance. It should be used
together with 'which_score'
- filename
- a character string naming a filename
- keep.significance
- logical to indicate whether or not to mask
those insignfiicant by NA. By default, it sets to true to mask those
insignfiicant by NA
Value
a data frame with following components:
setID: term ID
setSize: the number of genes in the set
name: term name
namespace: term namespace
distance: term distance
sample names: sample names in the next columns
Note
If "filename" is not NULL, a tab-delimited text file will be also
written out.
Examples
#output <- dGSEAwrite(eTerm, which_content="gadjp", which_score="gadjp", filename="eTerm.txt")