| geneqtl {GSAQ} | R Documentation |
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
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.
Author(s)
Samarendra Das
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)