cis.vs.trans.classification: A cis/trans classifier

In gap: Genetic Analysis Package

A cis/trans classifier

Description

A cis/trans classifier

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.

Details

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

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)

gap documentation built on Aug. 26, 2023, 5:07 p.m.