samplestats: Statistics for each F1 sample over all markers

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Statistics for each F1 sample over all markers

Description

Tabulate for each F1 sample in how many markers it has a missing, invalid or valid score.

Usage

samplestats(chk, scores, F1, qall_flavor="qall_mult",
qall_threshold=0, ploidy, ploidy2, scores_long=TRUE)

Arguments

chk	a data frame as returned by checkF1
scores	A data frame as read from the scores file produced by function fitMarkers of package fitPoly (or a subset with at least columns MarkerName, SampleName and geno), or a data frame as returned by function scores2wide. In the first case (default) parameter scores_long must be TRUE, in the second case it must be FALSE.
F1	character vector with the sample names of the F1 individuals
qall_flavor	which quality parameter column must be shown in compfile, default "qall_mult". If no quality data are wanted, specify "".
qall_threshold	only markers with a qall score > qall.threshold are included in the tabulation
ploidy	the ploidy of parent 1 (must be even, 2 (diploid) or larger), and the same as used by checkF1 to calculate the chk data frame
ploidy2	the ploidy of parent 2. If omitted it is assumed to be equal to ploidy. Should be the same as used by checkF1 to calculate the chk data frame
scores_long	TRUE if scores is in "long format", FALSE if it is in "wide format" (see parameter scores)

Value

A matrix with samples in rows and 3 columns: missing, invalid, valid, giving for each sample the number of markers where it has a missing, invalid or valid dosage score

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