GSAQ (version 1.0)

genedist: Chromosomal distribution of the genes in the selected geneset

Description

The function computes the chromosome wise distribution of the genes in the selected geneset and also plots the chromosomal distribution.

Usage

genedist(geneset, genelist, plot)

Arguments

geneset

geneset is a vector of characters representing the names of genes/ gene ids selected from the whole gene list 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 space: 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.

plot

plot is a character string indicating whether the chromosomal distribution of the genes in the selected geneset will be plotted or not. It can be either TRUE/FALSE.

Value

Examples

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