GSAQ (version 1.0)

geneqtl: List of the selected genes along with their corresponding overlapped QTL

Description

The function enables to obtain list of the selected genes along with the corresponding overlapped Quantitative Trait Loci (QTL) ids/names along with their genomic positions.

Usage

geneqtl(geneset, genelist, qtl)

Arguments

geneset

geneset is a vector of characters representing the names of genes/ gene ids selected from the whole gene list/space by using a gene selection method.

genelist

genelist is a N by 3 dataframe/ matrix (genes/gene ids as row names); where, N represents the number of genes in the whole gene set: first coloumn represnting the chromosomal location of genes: second coloumn representing the start position of genes in terms of basepairs: third coloumn representing the end position of genes in terms of basepairs in their respective chromosomes.

qtl

qtl is a Q by 3 dataframe/matrix (qtl names/qtl ids as row names);where, Q represents the number of qtls: first coloumn represnting the chromosomal location of qtls: second coloumn representing the start position of qtls in terms of basepairs: third coloumn representing the end position of qtls in terms of basepairs in their respective chromosomes.

Value

Examples

data(rice_salt)
data(genelist)
data(qtl_salt)
x=as.data.frame(rice_salt[-1,])
y=as.numeric(rice_salt[1,])
genelist=as.data.frame(genelist)
qtl=as.data.frame(qtl_salt)
geneset= GeneSelect(x, y, s=50, method="t-score")$selectgenes
geneqtl(geneset, genelist, qtl)