GMRP (version 1.0.0)

snpposit: SNP Position Annotation

Description

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

Usage

snpposit(SNPdata, SNP_hg19="chr", X="no",LG=10, main="A", maxd=2000)

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.

X

character parameter. It has Two options: X="yes" or X="no". Default is X="no".

LG

a numeric parameter that gives maximum permissible distance between positions.

main

a string which is title of graph. If no title is given, then man="".

maxd

maxd is a numeric parameter that is maximum distance for truncating chromosome columns. If there are not too big differences among 23 chromosomes, then maxd can be set to be larger than 2000.

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.

See Also

barplot, text, chrp

Examples

data(SNP358.data)
SNP358<-DataFrame(SNP358.data)
snpposit(SNPdata=SNP358,SNP_hg19="chr",X="Yes",LG=10,main="A",maxd=2000)