dnet (version 1.0.0)

dGSEAwrite: Function to write out enrichment results

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)

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

See Also

dGSEA

Examples

output <- dGSEAwrite(eTerm, which_content="gadjp", which_score="gadjp",
filename="eTerm.txt")