checkmrkDosage: check a marker dosages matrix or data.frame

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

Description

check a marker dosages matrix or data.frame, select columns and rows, convert to matrix

Usage

checkmrkDosage(mrkDosage, ploidy, indiv=NULL, markers=NULL,
generateMarkernames=TRUE)

Arguments

mrkDosage	matrix or data.frame. Markers are in rows, individuals in columns, each cell has a marker dosage. If mrkDosage is a matrix, the colnames are the individual names and the rownames are the marker names. If mrkDosage is a data.frame and the name of the first column starts with "marker" (upper/lowercase not relevant) the contents of this column are used as marker names, else the rownames are used as marker names. The (other) column names are the individual names. All marker dosages must be in 0:ploidy or NA.
ploidy	an integer value; all dosages are checked to be in 0:ploidy or NA
indiv	NULL (default) or a character vector with names of individuals to be selected. If NULL, all individuals are selected
markers	NULL (default) or a character vector with names of markers to be selected. If NULL, all markers are selected.
generateMarkernames	if TRUE (default) and mrkDosage has no markernames specified, markernames are generated automatically. Markernames must be either present or be generated, and none may be missing.

Details

This function is called by inferHaplotypes and by mergeReplicates, so normally there is no need for the user to call this function directly.

Value

a matrix with the selected columns in the order of indiv and the selected rows in order of markers (or all columns or rows in the original order if indiv or markers are not specified), with names of individuals as column names, marker names as row names

Examples

mrkdos <- data.frame(
 marker=paste0("mrk", 1:3),
 indiv1=c(1, 2, 2),
 indiv2=c(4, 0, 0),
 indiv3=c(3, 0, 2))
# use all rows and columns:
checkmrkDosage(mrkDosage=mrkdos, ploidy=4)
# use only first and last row and column and change the order:
checkmrkDosage(mrkDosage=mrkdos, ploidy=4, indiv=c("indiv3", "indiv1"),
              markers=c("mrk3", "mrk1"))

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