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Last data update: 2014.03.03

R: Mapping SNPs to Classes

map2class

R Documentation

Mapping SNPs to Classes

Description

The function maps SNPs to classes based on genome coordinates

Usage

map2class(coords, SNPs, extend.boundary = 0)

Arguments

`coords`	A data frame containing chromosome and upper and lower coordinates for a each class to be mapped. This must include column names 'chr', 'start', 'stop', and 'class'.
`SNPs`	A data frame containing genome coordinates of SNPs. This must include column names 'SNP', 'chr', 'position'.
`extend.boundary`	Number of base pairs to extend the class coordinates for mapping.

Details

Genomic coordinates defining the class boundaies in object, coors, and SNP location in object, SNPs should be annotated within the same build.

Note: That if using the map2class function to map SNPs to classes to use in the GenCAT function, then additional columns for effect_allele and other_allele can be used.

Value

A data frame with SNP information including class label.

Author(s)

Eric Reed, Sara Nunez, Jing Qian, Andrea Foulkes

Examples

data('CardioData')
data('coords')

######################
#Mapping SNPs to genes
######################
print(head(coords))

#Subset CardioData to decrease CPU time
CardioDataSub<-CardioData[CardioData$chr < 15,]
set.seed(1)
CardioDataSub<-CardioDataSub[sample(1:nrow(CardioDataSub), 100),]

print(head(CardioDataSub))

CardioMapped<-map2class(coords, CardioDataSub, extend.boundary = 5000)

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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Type 'q()' to quit R.

> library(GenCAT)
Loading required package: dplyr

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GenCAT/map2class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: map2class
> ### Title: Mapping SNPs to Classes
> ### Aliases: map2class
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> data('CardioData')
> data('coords')
> 
> ######################
> #Mapping SNPs to genes
> ######################
> print(head(coords))
  chr  start   stop    class
1   1  69090  70008    OR4F5
2   1 367658 368597 OR4F29-1
3   1 621095 622034 OR4F29-2
4   1 861120 879961   SAMD11
5   1 879582 894679    NOC2L
6   1 895966 901099   KLHL17
> 
> #Subset CardioData to decrease CPU time
> CardioDataSub<-CardioData[CardioData$chr < 15,]
> set.seed(1)
> CardioDataSub<-CardioDataSub[sample(1:nrow(CardioDataSub), 100),]
> 
> print(head(CardioDataSub))
             SNP effect_allele other_allele   testStat chr  position
28809 rs17076895             G            A -0.3420408  13  19756051
37688  rs1955633             G            T -0.4473971  14  58483217
57498  rs4772299             G            A -1.7237480  13 101147019
88758  rs9535722             C            A -0.7384099  13  52207488
19668 rs12886900             G            A  0.1953169  14  79443038
88135  rs9530612             C            A  0.8900307  13  77522290
> 
> CardioMapped<-map2class(coords, CardioDataSub, extend.boundary = 5000)
[1] "Mapping SNPs to classes on chromosome 13."
[1] "Mapping SNPs to classes on chromosome 14."
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>