dGSEAwrite: Function to write out enrichment results

In hfang-bristol/dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

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.

See Also

dGSEA

Examples

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

hfang-bristol/dnet documentation built on Feb. 23, 2020, 2:06 p.m.