genMOSSplus: Application of MOSS algorithm to genome-wide association study (GWAS)
Version 1.0

This is a genMOSS package with additional datafile preprocessing functions. Performs genome-wide analysis of dense SNP array data using the mode oriented stochastic search (MOSS) algorithm in a case-control design. The MOSS algorithm is a Bayesian variable selection procedure that is applicable to GWAS data. It identifies combinations of the best predictive SNPs associated with the response. It also performs a hierarchical log-linear model search to identify the most relevant associations among the resulting subsets of SNPs. This package also includes preprocessing of the data from Plink format to the format required by the MOSS algorithm.

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AuthorOlga Vesselova, Matthew Friedlander, Laurent Briollais, Adrian Dobra, Helene Massam.
Date of publication2013-08-30 20:05:41
MaintainerLaurent Briollais <laurent@lunenfeld.ca>
LicenseGPL-2
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("genMOSSplus")

Man pages

ex2plink: Convert example dataset to Plink format
genMOSSplus-package: Application of MOSS algorithm to dense SNP array data
genos.clean: Removes badly predicted SNPs by MaCH
genos.clean.batch: Removes badly predicted SNPs by MaCH for all files
get.data.dims: Obtains matrix dimensions
get.file.copy: Copies files from one directory to another
MOSS.GWAS: A function implementing the MOSS algorithm for the analysis...
pre0.dir.create: Generate working subdirectory structure
pre1.plink2mach: Convert Plink to MaCH input format
pre1.plink2mach.batch: Convert Plink to MaCH input format for all files
pre2.remove.genos: Remove genos with many empty values
pre2.remove.genos.batch: Remove genos with many empty values for all files
pre3.call.mach: Call MaCH imputation with and without Hapmap
pre3.call.mach.batch: Call MaCH imputation with and without Hapmap
pre4.combine.case.control: Combine CASE and CONTROL files
pre4.combine.case.control.batch: Combine CASE and CONTROL files for all files
pre5.genos2numeric: Categorize genotype data into 3 levels
pre5.genos2numeric.batch: Categorize genotype data into 3 levels for each file
pre6.merge.genos: Combine geno files across all chromosomes
pre7.add.conf.var: Append confounding variables
pre7.add.conf.var.unix: Append confounding variables using Linux
pre8.split.train.test: Split dataset into TRAIN and TEST files
pre8.split.train.test.batch: Split dataset into TRAIN and TEST files for all files
run1.moss: Runs MOSS regression algorithm
tune1.subsets: Imputes dense map of SNPs on chromosome regions with MaCH

Functions

MOSS.GWAS Man page Source code
MOSS.GWAS.main Source code
MOSS.Hierarchical Source code
binToDec Source code
call.mach Source code
call.mach.nohap Source code
call.mach.nohap.step1 Source code
call.mach.nohap.step2 Source code
checkArgsMOSS.GWAS Source code
clean.rsq.combine Source code
combine.same.chrom Source code
cvFunc Source code
decToBin Source code
diff.square.sum Source code
ex2plink Man page Source code
extract.chrom.dir Source code
extract.genos Source code
fill.empties Source code
findDualGenerators Source code
findFormula Source code
findGenerators Source code
findHierNeighbours Source code
findIndex Source code
findLogMargLik Source code
findModel Source code
findNeighbours Source code
fitInteractionModels Source code
genMOSSplus Man page
genMOSSplus-package Man page
genos.clean Man page Source code
genos.clean.batch Man page Source code
genos2numeric Source code
genos2numeric.batch Source code
get.chrom.num Source code
get.data.dims Man page Source code
get.ext Source code
get.file.copy Man page Source code
get.file.name Source code
get.hap.unzip Source code
get.hap.zip Source code
get.position Source code
getSubsets Source code
helper.rand.ints Source code
len.empty.vec Source code
logLaplace Source code
machout2id Source code
machout2machin Source code
makeModelHierarchical Source code
pali Source code Source code Source code
pre0.dir.create Man page Source code
pre1.plink2mach Man page Source code
pre1.plink2mach.batch Man page Source code
pre2.remove.genos Man page Source code
pre2.remove.genos.batch Man page Source code
pre3.call.mach Man page Source code
pre3.call.mach.batch Man page Source code
pre4.combine.case.control Man page Source code
pre4.combine.case.control.batch Man page Source code
pre5.genos2numeric Man page Source code
pre5.genos2numeric.batch Man page Source code
pre6.merge.genos Man page Source code
pre7.add.conf.var Man page Source code
pre7.add.conf.var.unix Man page Source code
pre8.split.train.test Man page Source code
pre8.split.train.test.batch Man page Source code
prettyFormula Source code
prettyHierFormula Source code
rand.ints Source code
rand.mask Source code
randomHierModel Source code
repRow Source code
run1.moss Man page Source code
subdir.create Source code
tune1.subsets Man page Source code

Files

inst
inst/exdata
inst/exdata/mach20CASE.mlgeno.tar.bz2
inst/exdata/chr20.hap.gz.tar.bz2
inst/exdata/chr20.annotation.txt.tar.bz2
inst/exdata/chr20.snps.tar.bz2
inst/exdata/mach20CASE.mlinfo.tar.bz2
inst/exdata/Identifiers_comma.csv.tar.bz2
inst/exdata/conf.txt.tar.bz2
inst/exdata/indices.ann.txt.tar.bz2
inst/exdata/mach20CONTROL.mlgeno.tar.bz2
inst/exdata/genotypes_10_90.txt.tar.bz2
inst/exdata/mach20CONTROL.mlinfo.tar.bz2
inst/doc
inst/doc/genMOSSplus-manual.pdf
src
src/c_code.c
NAMESPACE
demo
demo/00Index
demo/gendemo.R
R
R/prettyFormula.R
R/get.file.name.R
R/get.position.R
R/get.chrom.num.R
R/fitInteractionModels.R
R/call.mach.R
R/pre1.plink2mach.R
R/call.mach.nohap.R
R/genos.clean.R
R/genos2numeric.batch.R
R/pre3.call.mach.R
R/getSubsets.R
R/diff.square.sum.R
R/pre7.add.conf.var.unix.R
R/findDualGenerators.R
R/pre3.call.mach.batch.R
R/get.ext.R
R/checkArgsMOSS.GWAS.R
R/genos2numeric.R
R/pre1.plink2mach.batch.R
R/pre5.genos2numeric.R
R/tune1.subsets.R
R/pre4.combine.case.control.R
R/run1.moss.R
R/subdir.create.R
R/MOSS.Hierarchical.R
R/len.empty.vec.R
R/genos.clean.batch.R
R/pre4.combine.case.control.batch.R
R/binToDec.R
R/findGenerators.R
R/MOSS.GWAS.main.R
R/rand.ints.R
R/findIndex.R
R/get.hap.zip.R
R/repRow.R
R/pre7.add.conf.var.R
R/pre5.genos2numeric.batch.R
R/cvFunc.R
R/makeModelHierarchical.R
R/findHierNeighbours.R
R/pre8.split.train.test.batch.R
R/findModel.R
R/ex2plink.R
R/call.mach.nohap.step2.R
R/decToBin.R
R/call.mach.nohap.step1.R
R/logLaplace.R
R/extract.genos.R
R/pre8.split.train.test.R
R/pre2.remove.genos.R
R/get.hap.unzip.R
R/MOSS.GWAS.R
R/findFormula.R
R/machout2id.R
R/get.data.dims.R
R/machout2machin.R
R/pre6.merge.genos.R
R/pre2.remove.genos.batch.R
R/get.file.copy.R
R/findLogMargLik.R
R/randomHierModel.R
R/prettyHierFormula.R
R/clean.rsq.combine.R
R/pre0.dir.create.R
R/findNeighbours.R
MD5
DESCRIPTION
man
man/pre8.split.train.test.Rd
man/pre5.genos2numeric.batch.Rd
man/pre4.combine.case.control.batch.Rd
man/pre3.call.mach.Rd
man/genMOSSplus-package.Rd
man/MOSS.GWAS.Rd
man/pre0.dir.create.Rd
man/pre2.remove.genos.Rd
man/genos.clean.Rd
man/get.data.dims.Rd
man/tune1.subsets.Rd
man/pre3.call.mach.batch.Rd
man/pre7.add.conf.var.Rd
man/pre1.plink2mach.batch.Rd
man/pre8.split.train.test.batch.Rd
man/pre5.genos2numeric.Rd
man/pre4.combine.case.control.Rd
man/get.file.copy.Rd
man/pre1.plink2mach.Rd
man/genos.clean.batch.Rd
man/pre7.add.conf.var.unix.Rd
man/ex2plink.Rd
man/pre2.remove.genos.batch.Rd
man/pre6.merge.genos.Rd
man/run1.moss.Rd
genMOSSplus documentation built on May 29, 2017, 2:09 p.m.