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.

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

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

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