mrkdos2mrkdid: get marker dosage IDs from marker dosages

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

Description

get marker dosage IDs (mrkdid) from marker dosages

Usage

mrkdos2mrkdid(mrkDosage, indiv=NULL, ploidy, check=TRUE)

Arguments

mrkDosage	matrix or data.frame. Markers are in rows, individuals in columns, each cell has a marker dosage. Names of individuals are the column names, marker names are the row names or (if a data.frame) in a column named MarkerNames. All marker dosages must be in 0:ploidy or NA. If a data.frame, additional columns may be present.
indiv	NULL (default) or a character vector with names of individuals to be selected. If NULL, all columns are selected; if mrkDosage is a data.frame, that is probably not what is intended.
ploidy	all marker dosages are checked to be in 0:ploidy or NA
check	if TRUE (default) checkmrkDosage is called. If FALSE it is assumed that mrkDosage is a matrix (not a data.frame) and it is not checked.

Details

with ploidy==1 and (of course) all dosages 0 or 1 this function returns the haplotype numbers for the haplotype specified by each column

Value

a vector of marker dosage IDs, one for each column of mrkDosage: each a number in 1:((ploidy+1)^nrow(mrkDosage)), NA for each column in dosages where any of the dosages are NA

Examples

# dosages of 3 markers in 3 tetraploid individuals:
mrkdosg <-
 matrix(c(1,2,2, 4,0,0, 3,0,2), nrow=3,
        dimnames=list(c("mrkA", "mrkB", "mrkC"), c("indiv1", "indiv2", "indiv3")))
# get the "marker dosage IDs":
dids <- mrkdos2mrkdid(mrkDosage=mrkdosg, ploidy=4)
# convert dids back to marker dosages:
mrkdid2mrkdos(dosageIDs=dids, nmrk=3, ploidy=4, mrknames=c("mrkA", "mrkB", "mrkC"))

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