Learn R Programming

genMOSSplus (version 1.0)

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

Description

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.

Copy Link

Version

Install

install.packages('genMOSSplus')

Monthly Downloads

3

Version

1.0

License

GPL-2

Maintainer

Laurent Briollais

Last Published

August 30th, 2013

Functions in genMOSSplus (1.0)

pre2.remove.genos

Remove genos with many empty values

Runs MOSS regression algorithm

pre8.split.train.test.batch

Split dataset into TRAIN and TEST files for all files

pre5.genos2numeric

Categorize genotype data into 3 levels

pre4.combine.case.control

Combine CASE and CONTROL files

pre1.plink2mach.batch

Convert Plink to MaCH input format for all files

pre3.call.mach.batch

Call MaCH imputation with and without Hapmap

genos.clean.batch

Removes badly predicted SNPs by MaCH for all files

genMOSSplus-package

Application of MOSS algorithm to dense SNP array data

pre8.split.train.test

Split dataset into TRAIN and TEST files

Obtains matrix dimensions

pre0.dir.create

Generate working subdirectory structure

pre7.add.conf.var

Append confounding variables

Removes badly predicted SNPs by MaCH

Copies files from one directory to another

pre2.remove.genos.batch

Remove genos with many empty values for all files

Convert example dataset to Plink format

pre5.genos2numeric.batch

Categorize genotype data into 3 levels for each file

A function implementing the MOSS algorithm for the analysis of GWAS data.

Imputes dense map of SNPs on chromosome regions with MaCH

Call MaCH imputation with and without Hapmap

pre6.merge.genos

Combine geno files across all chromosomes

pre7.add.conf.var.unix

Append confounding variables using Linux

pre1.plink2mach

Convert Plink to MaCH input format

pre4.combine.case.control.batch

Combine CASE and CONTROL files for all files