AncestryMapper (version 2.0)

calculateAMids: Calculate genetic distances.

Description

calculates and assigns Ancestry Mapper Ids (AMids) in a more crude, but faster manner than calculateAMids

Usage

calculateAMids(pedtxtFile, fileReferences)

Arguments

pedtxtFile

Character vector giving path to PED file to be used. The PED file should include all 51 HGDP references and the individuals for which the user wishes to calculate the genetic distance.

fileReferences

Character vector giving path to file File detailing the individuals in the ped file that correspond to the references, and the populations they refer to. A file that uses the 51 HGDP reference populations is provided with the package.

Examples

## Not run: 
# library(AncestryMapper)
# 
# HGDP_References <- system.file('extdata',
#                                'HGDP_References.txt',
#                                 package = 'AncestryMapper')
# 
# 
# HGDP_500SNPs <- system.file('extdata',
#                             'HGDP_500SNPs.ped',
#                              package = 'AncestryMapper')
# 
# Corpheno <- system.file('extdata',
#                         'CorPheno',
#                          package = 'AncestryMapper')
# 
# genetic.distance <- calculateAMids(pedtxtFile = HGDP_500SNPs,
#                                    fileReferences = HGDP_References)
# 
# plotAMids(AMids = genetic.distance, phenoFile = Corpheno, columnPlot = "I")
# ## End(Not run)