dnet (version 1.1.7)

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) 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

See Also

dGSEA

Examples

# NOT RUN {
#output <- dGSEAwrite(eTerm, which_content="gadjp", which_score="gadjp", filename="eTerm.txt")
# }