mrkdid2mrkdos: get the marker dosages from mrkdids (marker dosage IDs)

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

Description

get the marker dosages from mrkdids (marker dosage IDs)

Usage

mrkdid2mrkdos(dosageIDs, nmrk, ploidy, mrknames=NULL)

Arguments

dosageIDs	vector of marker-dosage-combination IDs (mrkdid)
nmrk	character vector of marker names in the haploblock
ploidy	the ploidy level, a single positive integer
mrknames	a vector of nmrk marker names (default NULL): if not NULL these are used as rownames of the returned matrix

Value

a matrix with in columns the marker dosages corresponding to the marker dosageIDs, with these mrkdids as colnames, and one row per marker, with marker names as rownames if mrknames are specified

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.