myDNAScreenSNPS: Overlaps myDNA genotypes with SNPs of interest

In IngaPa/myDNA: myDNA: R package to analyze personal genotypes

Description

Overlaps myDNA genotypes with SNPs of interest

Usage

myDNAScreenSNPS(myDNA, snpsData)

Arguments

myDNA	(data.frame) analyzed genotypes, an output of importDNA function
snpsData	(data.frame) with min 2 columns: rsID (SNPid) and risk allele In that order!

Details

This function identifies overlap between my genotypes (myDNA object) and data.frame which stores info SNPs (their unique ID -rsID, and risk allele -in that order. This function is useful when user already has a list of SNPs associated with a trait of interest.

Examples

## Not run: 
# example - creating example for myDNAScreenSNPS()
# IDEA is as follows: extract rs and snp risk alleles, and extract those for
 coronary heart disease
 # filter CHD SNPS
dd.heart <- filter(db,
                   MAPPED_TRAIT=="coronary heart disease")

snpsData <-   dd.heart$STRONGEST.SNP.RISK.ALLELE
# greping risk allele
riskAlleles <- gsub("[^\\-]*-([ATCG?])", "\\1",
                    snpsData)

snpsData <- cbind(dd.heart$SNPS,riskAlleles)


# check my genome for given list of SNPs
myDNAScreenSNPS(myDNA, snpsData )

 
## End(Not run)

IngaPa/myDNA documentation built on Oct. 30, 2019, 7:22 p.m.