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Last data update: 2014.03.03

R: Assigns SNPs to genes

snps.to.genes

R Documentation

Assigns SNPs to genes

Description

Assigns SNPs to genes based on their physical distance.

Usage

snps.to.genes(snp.info, gene.info, distance)

Arguments

`snp.info`	A data frame with 3 columns with names: Name, Position and Chr that correspond to the SNP name, its position on the genome and its chromosome, respectively
`gene.info`	A data frame with 4 columns with names: Name, Start, End and Chr that correspond to the gene name, start and end positions on the genome and its chromosome, respectively
`distance`	A number that corresponds to the distance below and above the Start and End positions of the gene that all SNPs in that region should be assigned to the gene

Value

A list of the same size as the number of genes of the gene.info data frame. The names of the SNPs assigned to each gene are returned

Examples

data(SNPs)
data(genes)
snps.to.genes(snp.info=SNPs,gene.info=genes,distance=50)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(PAGWAS)
Loading required package: lars
Loaded lars 1.2

Loading required package: foreach
Loading required package: mnormt
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/PAGWAS/snps.to.genes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: snps.to.genes
> ### Title: Assigns SNPs to genes
> ### Aliases: snps.to.genes
> 
> ### ** Examples
> 
> data(SNPs)
> data(genes)
> snps.to.genes(snp.info=SNPs,gene.info=genes,distance=50)
$GENE1
character(0)

$GENE2
[1] "SNP50" "SNP65"

$GENE20
character(0)

$GENE3
[1] "SNP28" "SNP34" "SNP38"

$GENE4
[1] "SNP61" "SNP89"

$GENE5
[1] "SNP26" "SNP41" "SNP56" "SNP69" "SNP78" "SNP87"

$GENE6
[1] "SNP45" "SNP67" "SNP95"

$GENE7
[1] "SNP1"   "SNP77"  "SNP100"

$GENE8
[1] "SNP77"

$GENE9
[1] "SNP4"  "SNP6"  "SNP18" "SNP32" "SNP47" "SNP96"

$GENE10
[1] "SNP21" "SNP60" "SNP98"

$GENE11
[1] "SNP10" "SNP17" "SNP37" "SNP39" "SNP40"

$GENE12
[1] "SNP2"  "SNP25" "SNP49" "SNP64" "SNP76"

$GENE13
[1] "SNP97"

$GENE14
[1] "SNP5"  "SNP8"  "SNP36"

$GENE15
character(0)

$GENE16
character(0)

$GENE17
character(0)

$GENE18
character(0)

$GENE19
character(0)

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>