geneqtl: List of the selected genes along with their corresponding...
In GSAQ: Gene Set Analysis with QTL

Description Usage Arguments Value Author(s) Examples

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.

1	geneqtl(geneset, genelist, qtl)

`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.

The function returns a list with two components. First component returns the list of selected genes along with their overlapped QTL ids/names. Second component gives the list of selected genes with their overlapped QTL ids/names and their respective genomic positions.

Samarendra Das

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)