KeggPA: Kegg Human Pathway Analysis Based on Fisher's on tail exact...

Description Usage Arguments Details Value Author(s) Examples

Description

Kegg Human Pathway Analysis Based on Fisher's on tail exact test, overrepresentated pathways are found.

Usage

1
keggPA(hgnc, project_name, kegg.list = NULL)

Arguments

hgnc

a vector of Human Gene symbol IDs or entrez gene IDs in format of "hsa:XXXX"

project_name

a character stating name of the project used in writing the results file in the directory

kegg.list

is a dataframe in format of Kegg Pathway ID, entrez IDs, Gene Symbol IDs and Name of Pathway obtained from kegg directory. By default December 2013 version will be used

Details

Based on assumptions of hypergeometric test, we omit all the genes that are not in kegg database. The hypergeometric p-value is calcualted based on total genes in annotated in kegg database.

Value

A dataframe of pathway IDs, pathway names, mapped genes, p-values and FDRs.

Author(s)

Mehran Karimzadeh

Examples

1
keggPA(c("BRCA1","BRCA2","TP53","XRCC5"),project_name="Example_please_delete")

mehrankr/KeggPA documentation built on May 22, 2017, 3:28 a.m.