R: function to subset objects of class scan.gwaa and...

snp.subset {GenABEL} | R Documentation

## function to subset objects of class scan.gwaa and check.marker

### Description

Computing objects of class scan.gwaa may take long, especially when haplotypic analysis is performed. Therefore this function helps substracting results on some region (indicated by list of SNPs)

### Usage

    snp.subset(data, snpsubset)

### Arguments

`data` | object of class `scan.gwaa-class` or `check.marker-class`
`snpsubset` | character vector of snps to select

### Value

Object of class `scan.gwaa-class` or `check.marker-class`

### Author(s)

Yurii Aulchenko

### See Also

`scan.gwaa-class`, `check.marker-class`

### Examples

    require(GenABEL.data)
    data(srdta)
    # processing check.marker object
    #mc <- check.marker(data=srdta@gtdata[,1:100],redundant="all",maf=0.01,
    # minconcordance=0.9,fdr=.1,ibs.mrk=0)
    mc <- check.marker(data=srdta@gtdata[,1:100],maf=0.01,fdr=.1,ibs.mrk=0)
    summary(mc)
    #plot(mc)
    mc1 <- snp.subset(mc,snps=srdta@gtdata@snpnames[20:50])
    summary(mc1)
    #plot(mc1)
    # processing scan.gwaa object
    a <- qtscore(qt3~sex+age,data=srdta)
    plot(a)
    a1 <- snp.subset(a,snps=srdta@gtdata@snpnames[10:20])
    plot(a1)

[Package GenABEL version 1.8-0 Index]