Description Usage Arguments Value Author(s) References See Also Examples
Get the p-value of GATES-Simes. It uses an extended Simes procedure to combine GATES p-values across multiple genes in a pathway.
1 | GatesSimes(pvec, ldmatrix, snp.info, gene.info)
|
pvec |
p-values for each SNP. |
ldmatrix |
numeric. A correlation matrix of SNPs with dimensions matching the length of pvec (the number of SNPs). |
snp.info |
SNP information matrix, the 1st column is SNP id, 2nd column is chromosome #, 3rd column indicates SNP location. |
gene.info |
GENE information matrix, The 1st column is GENE id, 2nd column is chromosome #, 3rd and 4th column indicate start and end positions of the gene. |
A p-value.
Il-Youp Kwak and Wei Pan
Hongsheng Gui, Miaoxin Li, Pak C Sham and Stacey S Cherny (2011) Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn's Disease BMC Research Notes, 4:386
1 2 3 4 5 6 7 8 9 10 | #simula <- simPathAR1Snp(nGenes=20, nGenes1=1, nSNPlim=c(1, 20), nSNP0=1:3,
# LOR=.2, rholim=c(0,0),
# n=30, MAFlim=c(0.05, 0.4), p0=0.05)
#logitp <- getlogitp(simula$Y, simula$X)
## get correlation of SNPs using controls
#ldmat <- cor(simula$X[ simula$Y == 0, ])
#out <- GatesSimes(pvec = logitp, ldmatrix = ldmat, snp.info = simula$snp.info,
# gene.info = simula$gene.info)
#out
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