boostSeq: Optimized GWAS cohort subset selection for resequencing studies

This package contains functionality to select a subsample of a genotyped cohort e.g. from a GWAS that is preferential for resequencing under the assumtion that causal variants share a haplotype with the risk allele of associated variants. The subsample is selected such that is contains risk alleles at maximum frequency for all SNPs specified. Phentoypes can also be included as additional variables to obtain a higher fraction of extreme phenotypes. An arbitrary number of SNPs and/or phentoypes can be specified for enrichment in a single subsample.

Author
c(person("Milan Hiersche", "Developer", email = "mihi@uni-muenster.de")
Date of publication
2012-08-11 15:09:33
Maintainer
Milan Hiersche <mihi@uni-muenster.de>
License
GPL (>= 2)
Version
1.0
URLs

View on CRAN

Man pages

alleleEnrichment
Select a Subsample with Optimized Allele Frequencies from...
getSnpWeights
Extract p-value weights from a GWAS resultfile

Files in this package

boostSeq
boostSeq/MD5
boostSeq/man
boostSeq/man/alleleEnrichment.Rd
boostSeq/man/getSnpWeights.Rd
boostSeq/R
boostSeq/R/alleleEnrichment.data.R
boostSeq/R/getGenotypes.R
boostSeq/R/alleleEnrichment.R
boostSeq/R/alleleEnrichment.perm.R
boostSeq/R/alleleEnrichment.lp.R
boostSeq/R/getSnpWeights.R
boostSeq/NAMESPACE
boostSeq/inst
boostSeq/inst/extdata
boostSeq/inst/extdata/example.ped
boostSeq/inst/extdata/example.pheno
boostSeq/inst/extdata/example.map
boostSeq/inst/extdata/example.gwas
boostSeq/DESCRIPTION