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

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.

Author
Olga Vesselova, Matthew Friedlander, Laurent Briollais, Adrian Dobra, Helene Massam.
Date of publication
2013-08-30 20:05:41
Maintainer
Laurent Briollais <laurent@lunenfeld.ca>
License
GPL-2
Version
1.0

View on CRAN

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

Files in this package

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