R: A cis/trans classifier

cis.vs.trans.classification {gap} | R Documentation

## A cis/trans classifier

### Description

The function classifies variants into cis/trans category according to a panel which contains id, chr, start, end, gene variables.

### Usage

    cis.vs.trans.classification(hits, panel, id, radius = 1e+06)

### Arguments

`hits` | Data to be used, which contains prot, Chr, bp, id and/or other information such as SNPid.
`panel` | Panel data.
`id` | Identifier.
`radius` | The flanking distance for variants.

### Value

The cis/trans classification.

### Author(s)

James Peters

### Examples

    cis.vs.trans.classification(hits=jma.cojo, panel=inf1, id="uniprot")
    ## Not run:
    INF <- Sys.getenv("INF")
    f <- file.path(INF,"work","INF1.merge")
    clumped <- read.delim(f,as.is=TRUE)
    hits <- merge(clumped[c("CHR","POS","MarkerName","prot","log10p")],
                  inf1[c("prot","uniprot")],by="prot")
    names(hits) <- c("prot","Chr","bp","SNP","log10p","uniprot")
    cistrans <- cis.vs.trans.classification(hits,inf1,"uniprot")
    cis.vs.trans <- with(cistrans,data)
    knitr::kable(with(cistrans,table),caption="Table 1. cis/trans classification")
    with(cistrans,total)

    ## End(Not run)

[Package gap version 1.2.3-6 Index]