expandUnknownParents: Generate markers with all combinations of parental scores

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Generate markers with all combinations of parental scores

Description

For markers where the segregation type in the F1 is known but the parental consensus scores are missing, this function generates multiple versions of the marker, each with a different combination of parental scores matching the segregation and a different suffix to the marker name.

Usage

expandUnknownParents(scores, sep="@",
polysomic=TRUE, disomic=FALSE, mixed=FALSE,
ploidy, ploidy2, scorefile)

Arguments

scores	a data frame as returned by writeDosagefile, or the combscores item in the return value of compareProbes or removeRedundant
sep	a short string (one or more characters, default "@") to separate the original marker name from the consecutive letters (a, b, c etc) that identify the different versions of the marker. Markers that already have parental scores are not modified
polysomic	TRUE or FALSE; should be the same as used by checkF1
disomic	TRUE or FALSE; should be the same as used by checkF1
mixed	TRUE or FALSE; should be the same as used by checkF1
ploidy	the ploidy of parent 1 (must be even, 2 (diploid) or larger), and the same as used by checkF1
ploidy2	the ploidy of parent 2. If omitted it is assumed to be equal to ploidy. Should be the same as used by checkF1
scorefile	a filename to which the result is written; if NA no file is written

Value

A data frame with the same format and contents as parameter scores, with each marker where parental scores were missing expanded to multiple rows, one per parental dosage combination

fitPoly documentation built on April 3, 2025, 8:58 p.m.