| correctDosages {polymapR} | R Documentation |
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, dosage_matrix, parent1, parent2, ploidy,
polysomic=TRUE, disomic=FALSE, mixed=FALSE,
absent.threshold=0.04)
Arguments
chk |
data frame returned by function checkF1 when called without shiftmarkers |
dosage_matrix |
An integer matrix with markers in rows and individuals in columns. |
parent1 |
character vector with names of the samples of parent 1 |
parent2 |
character vector with names of the samples of parent 2 |
ploidy |
ploidy of parents and F1 (correctDosages must not be used for F1 populations where the parents have a different ploidy, or where the parental genotypes are not scored together with the F1); same as used in the call to checkF1 that generated data.frame chk |
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 |
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 |
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)