pedigreeSim2PH {PolyHaplotyper}

convert the PedigreeSim true haplotypes to marker dosages and haplotype dosages

Description

convert the PedigreeSim true haplotypes to marker dosages and haplotype dosages

Usage

pedigreeSim2PH(ps_geno, haploblock, indiv=NULL, dropUnused=TRUE)

Arguments

ps_geno

the filename of a *_genotypes.dat file as produced by PedigreeSim, or a data.frame read from such a file (with a column marker, followed by <ploidy> columns per individual with the marker alleles for each homolog; the names of these columns must be <indivname>_<homolog number>). ps_geno should not contain missing data (this will be true unless the PedigreeSim output is midified)

haploblock

a list of character vectors. The names are the names of the haploblocks, the character vectors have the names of the markers in each haploblock. Haplotype names are constructed from the haploblock names, which are used as prefixes to which the (zero-padded) haplotype numbers are are appended with separator '_'.
All markers in haploblock must be present in ps_geno. If haploblock is NULL only the marker dosages are generated, not the haplotype dosages.

indiv

the names of the individuals to be extracted; default NULL: all individuals in ps_geno. If not NULL, all indiv must be present in ps_geno

dropUnused

TRUE (default) if the returned matrix should only contain rows for haplotypes that are present; if FALSE matrix contains rows for all possible haplotypes

Details

if all alleles are in 0/1, these are kept. If only 2 allele symbols occur in ps_geno all are converted (alphabetically) to 0/1 in the same way (e.g. if the alleles are A and B, A -> 0 and B -> 1, even in markers with only B's). If different allele symbols are used between markers, per marker the (alphabetically or numerically) lowest -> 0 and the highest -> 1. So if more than two different allele symbols occur in ps_geno, and one marker has only A and another only B alleles, both are converted to 0's.
in mrkDosage, the dosage of the alleles (converted to) 1 is reported

Value

a list with 2 items:
$mrkDosage: a matrix of marker dosages in the input format of inferHaplotypes, with all markers that occur in haploblock, sorted according to haploblock, and for the selected indiv in the specified order
$haplist: (only if haploblock is not NULL) a list with one element for each haploblock, similar to the inferHaplotypes output). Each element is itself a list, with two components:
$hapdos is a matrix with the haplotype dosages for that haploblock for each individual
$markers: a vector with the names of the markers in the haploblock in the output of inferHaplotypes