genedist {GSAQ} | R Documentation |
The function computes the chromosome wise distribution of the genes in the selected geneset and also plots the chromosomal distribution.
genedist(geneset, genelist, plot)
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. |
The function returns the chromosomal distribution of the genes in the selected geneset.
Samarendra Das
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)