R/utility_functions.R

In bahlolab/moimix: Estimating mulitplicity of infection from high-throughput sequencing data

# Title: utility_functions.R
# Author: Stuart Lee, Katherine Smith
# Description: Utility functions for the haldane package
#--- Datasets

#' Minor Allele Frequenies of ~ 30,000 Plasmodium falciparum SNPs.
#'
#' A dataset containing information about exonic SNPs in Plasmodium falciparum
#' from Manske et al., 2012 \url{http://www.ncbi.nlm.nih.gov/pubmed/22722859}.
#'
#' @name maf_summary
#' @docType data
#' @format A data frame with 29621 rows and 10 variables:
#' @source \url{http://www.malariagen.net/data}
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#' Plasmodium falciparum SNV data from Gambia.
#' 
#' Variant calls of polymorphic variants from 65 P.falciparum isolates in The Gambia,
#' from Amambua-Ngwa A, Tetteh KK et al., 2012 \url{http://www.ncbi.nlm.nih.gov/pubmed/23133397}.
#' The data was extracted from VCF files and converted to GDS format from Malaria Genomics Consortium Pf3k version 4. See the README file
#' at \url{ftp://ngs.sanger.ac.uk/production/pf3k/release_4/} for details. The GDS object was obtained
#' by filtering the MalariaGen VCF files and keeping only biallelic SNPs that were polymorphic in The Gambia
#' and passed all filters.  
#' 
#' @name gambian_isolates
#' @docType data
#' @format A \code{\link[SeqArray]{SeqVarGDSClass}} object.
#' @source \url{ftp://ngs.sanger.ac.uk/production/pf3k/release_4/}
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#' @import graphics methods utils stats
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