dGSEAwrite {dnet}R Documentation

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) 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:

Note

If "filename" is not NULL, a tab-delimited text file will be also written out.

See Also

dGSEA

Examples

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

[Package dnet version 1.1.3 Index]