AncestryMapper (version 2.0)

calculateAMidsArith: Calculate genetic distances.

Description

Calculates genetic distance between samples and population references.

Usage

calculateAMidsArith(pathTotpeds, pathToAriMedoids, AMmcapply = F, nrcores, seqchip = "", noseqdat = F, wd, NameOut = NULL, pathAll00)

Arguments

pathTotpeds

Character vector giving path to folder containing the plink tPED file(s) to be used.

pathToAriMedoids

Character vector giving path to folder containing the arithmetic references to be used.

AMmcapply

Logical value (TRUE or FALSE), specifying if the multicore funcion mcapply, should be used. Inappropriate for most HPC cluster systems. Default = FALSE

nrcores

Numeric value detailing how many cores should be used if AMmcapply==TRUE. If left unspecificed the number of cores will be detected and nrcores will be set to that number -2.

seqchip

Character vector specifying if only references from one main SNP chip panel are to be used. All references are marked with what chip panel they use at the end of their file names, eg 'Yoruba.HGDP.20000.Illumina.ods' May be important if your data has few SNPs in common with one panel. All toy references prepared use 'Illumina' panels. Whole Genome sequence data is specified with 'WG'. Supports custom designations, but will trigger a warning when used.

noseqdat

Logical value (TRUE or FALSE), specifying if sequence data is to be excluded, will use only references that do not have names ending in '.WG.ods/rds/rda'. Default = FALSE

wd

Character vector giving the desired working directory to house the outputs of calculateAMidsArith. If left unspecified will use current working directory.

NameOut

Character vector giving the desired prefix name for the AMid file. Default is NULL.

pathAll00

Character vector giving the path to a file containing the full data table of each dbSNP and both alleles. An example version covering the SNPs used in the example data is included. A full version can be found at: http://bit.ly/1OUstDP

Examples

## Not run: 
# Refs <- system.file('data', package = 'AncestryMapper')
# tpeds <- system.file('extdata', package = 'AncestryMapper')
# Corpheno <- system.file('extdata', 'CorPheno', package = 'AncestryMapper')
# All00Frq <- system.file ('data', 'MinMaxFreq.rda', package = 'AncestryMapper')
# 
# genetic.distance <- calculateAMidsArith(pathTotpeds = tpeds,
#                                    NameOut = 'Example',
#                                    pathToAriMedoids = Refs,
#                                    pathAll00 = All00Frq)
# 
# plotAMids(AMids = genetic.distance, phenoFile = Corpheno, columnPlot = "I")
# ## End(Not run)