| genedist {GSAQ} | R Documentation |
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
The function returns the chromosomal distribution of the genes in the selected geneset.
Author(s)
Samarendra Das
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)