correctDosages: Check if dosage scores may have to be shifted

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Check if dosage scores may have to be shifted

Description

fitPoly sometimes uses a "shifted" model to assign dosage scores (e.g. all samples are assigned a dosage one higher than the true dosage). This happens mostly when there are only few dosages present among the samples. This function checks if a shift of +/-1 is possible.

Usage

correctDosages(chk, scores, parent1, parent2, ploidy, ploidy2,
polysomic=TRUE, disomic=FALSE, mixed=FALSE, parentsScoredWithF1,
absent.threshold=0.04, outfile=NA)

Arguments

chk	data frame returned by function checkF1 when called without shiftmarkers
scores	data.frame with scores as produced by the fitMarkers function of package fitPoly; at least columns MarkerName, SampleName and geno must be present, any other columns are ignored
parent1	character vector with names of the samples of parent 1
parent2	character vector with names of the samples of parent 2
ploidy	The ploidy of parent 1 (must be even, 2 (diploid) or larger).
ploidy2	The ploidy of parent 2. If omitted it is assumed to be equal to ploidy.
polysomic	if TRUE at least all polysomic segtypes are considered; if FALSE these are not specifically selected (but if e.g. disomic is TRUE, any polysomic segtypes that are also disomic will still be considered); same as used in the call to checkF1 that generated data.frame chk
disomic	if TRUE at least all disomic segtypes are considered (see param polysomic); same as used in the call to checkF1 that generated data.frame chk
mixed	if TRUE at least all mixed segtypes are considered (see param polysomic). A mixed segtype occurs when inheritance in one parent is polysomic (random chromosome pairing) and in the other parent disomic (fully preferential chromosome pairing); same as used in the call to checkF1 that generated data.frame chk
parentsScoredWithF1	single logical. TRUE means that parents are scored in the same experiment and the same fitPoly run as the F1, else FALSE. If missing and ploidy2==ploidy, TRUE is assumed. If FALSE, parental scores will not be shifted along with the F1 scores.
absent.threshold	the threshold for the fraction of ALL samples that has the dosage that is assumed to be absent due to mis-fitting of fitPoly; should be at least the assumed error rate of the fitPoly scoring assuming the fitted model is correct
outfile	file name to which the result is written. If NA no file is written.

Details

A shift of -1 (or +1) is proposed when (1) the fraction of all samples with dosage 0 (or ploidy) is below absent.threshold, (2) the bestfit (not bestParentfit!) segtype in chk has one empty dosage on the low (or high) side and more than one empty dosage at the high (or low) side, and (3) the shifted consensus parental dosages do not conflict with the shifted segregation type.
The returned data.frame (or a subset, e.g. based on the values in the fracNotOk and parNA columns) can serve as parameter shiftmarkers in a new call to checkF1.
Based on the quality scores assigned by checkF1 to the original and shifted versions of each marker the user can decide if either or both should be kept. A data.frame combining selected rows of the original and shifted versions of the checkF1 output (which may contain both a shifted and an unshifted version of some markers) can then be used as input to compareProbes or writeDosagefile.

Value

a data frame with columns

• markername

• segtype: the bestfit (not bestParentfit!) segtype from chk

• parent1, parent2: the consensus parental dosages; possibly low-confidence, so may be different from those reported in chk

• shift: -1, 0 or 1: the amount by which this marker should be shifted

The next fields are only calculated if shift is not 0:

• fracNotOk: the fraction of ALL samples that are in the dosage (0 or ploidy) that should be empty if the marker is indeed shifted.

• parNA: the number of parental dosages that is missing (0, 1 or 2)

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