gap (version 1.5-1)

cis.vs.trans.classification: 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)

Value

The cis/trans classification.

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.

Author

James Peters

Examples

cis.vs.trans.classification(hits=jma.cojo, panel=inf1, id="uniprot")
if (FALSE) {
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)
}