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.

Install the latest version of this package by entering the following in R:
install.packages("genMOSSplus")
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

Functions

ex2plink Man page
genMOSSplus Man page
genMOSSplus-package Man page
genos.clean Man page
genos.clean.batch Man page
get.data.dims Man page
get.file.copy Man page
MOSS.GWAS Man page
pre0.dir.create Man page
pre1.plink2mach Man page
pre1.plink2mach.batch Man page
pre2.remove.genos Man page
pre2.remove.genos.batch Man page
pre3.call.mach Man page
pre3.call.mach.batch Man page
pre4.combine.case.control Man page
pre4.combine.case.control.batch Man page
pre5.genos2numeric Man page
pre5.genos2numeric.batch Man page
pre6.merge.genos Man page
pre7.add.conf.var Man page
pre7.add.conf.var.unix Man page
pre8.split.train.test Man page
pre8.split.train.test.batch Man page
run1.moss Man page
tune1.subsets Man page

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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