gene.list: List to describe the gene-SNP file

In ARTP: Gene and Pathway p-Values Computed using the Adaptive Rank Truncated Product

Description

The list to describe the gene-SNP file for ARTP_pathway

Format

The format is a list:

file

Text file containing at least 2 columns, where one column is for the SNPs and the other column is for the gene containing the SNP. No default.

delimiter

The delimiter used in file.

gene.var

Variable name or column number of the gene variable. The default is "Gene".

snp.var

Variable name or column number of the SNP variable. The default is "SNP".

chrm.var

Variable name or column number of the chromosome variable. The default is "Chr". This option is only used for calling plot_genes.

header

0 or 1 to denote if file contains a header of variable names. The default is 1.

Details

All the genes and SNPs listed in this file define a single pathway.

ARTP documentation built on May 2, 2019, 6:51 a.m.