snpPositAnnot: _SNP_ Position Annotation

In GMRP: GWAS-based Mendelian Randomization and Path Analyses

Description

This function is used to perform position annotation analysis of SNPs chosen from GWAS.

Usage

snpPositAnnot(SNPdata, SNP_hg19="chr", main)

Arguments

SNPdata	SNPdata may be hg19 that is a string vector(chr##.########) or two numeric vectors (chromosome number and SNP position).
SNP_hg19	a string parameter. It may be "hg19" or "chr". If SNP_hg19="hg19",then SNPdata contain a string vector of hg19 or if SNP_hg19="chr", then SNPdata consist of at lest two columns: chr and posit. chr is chromosome number and posit is SNP physical position on chromosomes. If data sheet has chromosome X, then character "X" should be changed to 23 in chr vector or chr23.######## in hg19 vector.
main	a string which is title of graph. If no title is given, then main="".

Value

Return a set of numbers of SNPs between which interval length > LG on 23 chromosomes. This function also creates a histogram for averaged distances between SNPs and SNP numbers on chromosomes.

Note

This function can also be applied to hg18 data with SNP_hg19="hg18".

Author(s)

Yuan-De Tan [e-mail]

See Also

barplot, text, chrp

Examples

data(SNP358.data)
SNP358<-DataFrame(SNP358.data)
snpPositAnnot(SNPdata=SNP358,SNP_hg19="chr",main="A")

GMRP documentation built on Nov. 8, 2020, 5:58 p.m.