GSAQ {GSAQ}

Gene Set Analysis with Quantitative Trait Loci with gene sampling model

Description

The function computes the statistical significance value (p-value) from gene set analysis test with QTL for the test H0: Genes in the selected geneset are at most as often overlapped with the QTL regions as the genes in not selected geneset; against H1: Genes in the geneset are more often overlapped with the QTL regions as compared to genes in not selected geneset.

Usage

GSAQ(geneset, genelist, qtl, SampleSize, K, method)

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.

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.

SampleSize

SampleSize is a numeric constant representing the size of the gene sample drawn from the geneset using the gene sampling model (SampleSize must be less than the size of geneset).

K

K is a numeric constant representing the number of gene samples of size equal to SampleSize will be drawn by the using gene sampling model.

method

method is a character string indicating which method for final p-value (combining p-values for various gene samples) is to be computed. One of "meanp", "sump", "logit", "sumz"or "logp" (default) can be abbreviated and used.

Value

The function returns the final statistical significance value (p-value) from Gene set Analysis with QTL test.

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
GSAQ(geneset, genelist, qtl, SampleSize=30, K=50, method="meanp")