snpPositAnnot: _SNP_ Position Annotation

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/snpPositAnnot.R

Description

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

Usage

1
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 [email protected]

See Also

barplot, text, chrp

Examples

1
2
3
data(SNP358.data)
SNP358<-DataFrame(SNP358.data)
snpPositAnnot(SNPdata=SNP358,SNP_hg19="chr",main="A")

GMRP documentation built on May 27, 2018, 6 p.m.