GSAQ {GSAQ} | R Documentation |
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")