CeRNASeek (version 2.1.3)

ceRNA.enrich: Enrich the biological functions of interest.

Description

Downstream analysis function of ceRNA,This function can be used to identify biological functions of interest, and users can enrich the functions of interest by ceRNA.enrich.

Usage

ceRNA.enrich(data, GOterms, background, threshold = 2, correction = "BH")

Arguments

data

a dataframe that the ceRNA relationship is the data, and the prediction result data obtained according to the ceRNA prediction algorithm.Such as ceRNA.cmi prediction result file.

GOterms

a list that goterm of interest and all gene sets in the term.

background

a vector containing a gene set in which GOterm annotated genes must be.Its id style must be consistent with the id format in GOterms.

threshold

a numeric (default 2) representing min number of intersection between a modulator's targets and a GOterms genes.

correction

correction method (default "BH") in one of p.adjust.methods.

Value

A list of identified miRNA sponge interactions containing following components:

• target represented target names,respectively.

• GOterm the GOterm name.

• target_num names of represented target in the triplet.

• GOtermnum the gene number of a GOterm;

• term_tar the number of intersected factor between a GOterm genes and a modulator targets;

• P_value the p value of the significance enrichment;

• fdr corrected P_value by the assigned method;

Details

Note:All the arguments without default value must be assigned.

Examples

# NOT RUN {
##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
ceRNA.enrich(data=dataset[["Pre.ceRNA"]],GOterms=dataset[["GOterms"]],
             background=dataset[["background"]],threshold=1,correction="BH")
# }