dGSEAwrite {dnet} | R Documentation |
dGSEAwrite
is supposed to write out enrichment results.
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 )
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 |
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
If "filename" is not NULL, a tab-delimited text file will be also written out.
#output <- dGSEAwrite(eTerm, which_content="gadjp", which_score="gadjp", filename="eTerm.txt")