Description Usage Arguments Details Value Author(s) Examples
Kegg Human Pathway Analysis Based on Fisher's on tail exact test, overrepresentated pathways are found.
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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 |
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.
A dataframe of pathway IDs, pathway names, mapped genes, p-values and FDRs.
Mehran Karimzadeh
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