create.pathway.df: Creates a pathway data frame

In PAGWAS: Pathway Analysis Methods for Genomewide Association Data

Description

Returns a data frame with L rows and M columns. L is the number of SNPs in the genotypes data frame and M is the number of tested pathways.

Usage

create.pathway.df(genotypes,snps.paths)

Arguments

genotypes	Genotype matrix, with L SNPs (columns) and N individuals (rows)
snps.paths	A list with entries the SNP members of each pathway. The size of the list is M

Value

A data frame with columns equal to the number of pathways in the pathway.snps list and rows equal to the number of tested SNPs

See Also

SNPs, genes, snps.to.pathways snps.to.genes

Examples

data(SNPs)
data(genes)
data(pathways)
data(genotypes)
snps.genes <- snps.to.genes(snp.info=SNPs,gene.info=genes, distance=0)
pathway.snps <- snps.to.pathways(pathways,snps.genes)
P <- create.pathway.df(genotypes=genotypes,snps.paths=pathway.snps)

Example output

Loading required package: lars
Loaded lars 1.2

Loading required package: foreach
Loading required package: mnormt

PAGWAS documentation built on May 2, 2019, 3:26 p.m.