build_ahccompletelist: generate a list with all haplotype combinations

In PolyHaplotyper: Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Description

generate a list which contains for each marker dosage combination at a given ploidy all matching haplotype combinations

Usage

build_ahccompletelist(ploidy, maxmrk, savesec=1800, printsec=300,
overwrite, shorten=FALSE)

Arguments

ploidy	ploidy; may be even or odd, but inferHaplotypes only works with even ploidy if FS families are present, so building an ahccompletelist for odd ploidy is probably not useful
maxmrk	the list will countain all haplotype combinations for haploblocks of 1...maxmrk markers
savesec	default 1800: number of seconds between successive saves of the intermediate results
printsec	default 300: number of seconds between printout of the current set of haplotypes. NA or 0 suppresses printing.
overwrite	the new file ahccompletelist_<ploidy>x.RData is written in the working directory. If a file with that name already exists and would be changed, this is aborted and the old file maintained if overwrite is FALSE
shorten	if file ahccompletelist_<ploidy>x.RData already exists and covers haploblocks of lengths longer than maxmrk, this file is left unchanged if shorten is FALSE (default), but is shortened to maxmrk if shorten is TRUE

Details

An ahccompletelist reduces the processing time of inferHaplotypes enormously but takes a long time to build. This should therefore be done when PolyHaplotyper will be used multiple times.
If an ahccompletelist file already exists in the working directory, this file is used as starting point; if maxmrk is larger than the length of the existing list only the additional items are calculated.
If this function crashes (due to exceeding the memory limits of the computer or of R) the file ahccompletelist_<ploidy>x.RData in the working directory contains an intact version of the ahccompletelist for the last finished marker count. Also, the temporary file "buildAHCcompletelist_<datetime>"_"<nmrk>.RData" contains a part of the list item for the number of markers being calculated at that moment.
Note that this function takes lots of time and memory already for ploidy 4 / maxmrk 7 and ploidy 6 / maxmrk 5, and is not practicable above ploidy 4 / maxmrk 8, ploidy 6 / maxmrk 6, ploidy 8 / maxmrk 5. Also, the files are large and take up considerable memory, and most of the size is used for the largest haploblock size. Therefore maxmrk should not be taken larger than necessary.

Value

NULL (invisible); the actual result is a file in the working directory named ahccompletelist_<ploidy>x.RData

Examples

# this example will create a file ahccompletelist_4x.RData
# in the working directory, for ploidy=4x and 1 - 4 markers:
build_ahccompletelist(ploidy=4, maxmrk=4, overwrite=FALSE)

PolyHaplotyper documentation built on June 17, 2021, 5:12 p.m.