ceRNA.enrich {CeRNASeek} | R Documentation |
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.
ceRNA.enrich(data, GOterms, background, threshold = 2, correction = "BH")
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 |
Note:All the arguments without default value must be assigned.
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;
##---- 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")