PLIS: Multiplicity control using Pooled LIS statistic

PLIS is a multiple testing procedure for testing several groups of hypotheses. Linear dependency is expected from the hypotheses within the same group and is modeled by hidden Markov Models. It is noted that, for PLIS, a smaller p value does not necessarily imply more significance because of dependency among the hypotheses. A typical application of PLIS is to analyze genome wide association studies datasets, where SNPs from the same chromosome are treated as a group and exhibit strong linear genomic dependency.

Author
Zhi Wei & Wenguang Sun
Date of publication
2012-08-11 04:40:46
Maintainer
Zhi Wei <zhiwei04@gmail.com>
License
GPL-3
Version
1.1

View on CRAN

Man pages

bwfw1.hmm
backward and forward inferences
bwfw.hmm
backward and forward inferences
em.hmm
EM algorithm for HMM to estimate LIS statistic
GWAS.SampleData
Sample GWAS Dataset
plis
A multiple testing procedure based on pooled LIS statistics
PLIS-package
PLIS

Files in this package

PLIS
PLIS/MD5
PLIS/R
PLIS/R/plis.R
PLIS/R/em.hmm.R
PLIS/R/bwfw1.hmm.R
PLIS/R/bwfw.hmm.R
PLIS/NAMESPACE
PLIS/man
PLIS/man/plis.Rd
PLIS/man/PLIS-package.Rd
PLIS/man/GWAS.SampleData.Rd
PLIS/man/em.hmm.Rd
PLIS/man/bwfw1.hmm.Rd
PLIS/man/bwfw.hmm.Rd
PLIS/DESCRIPTION
PLIS/data
PLIS/data/GWAS.SampleData.rda