rscharpf/MinimumDistance — Issue #8: motherPhenoData Duplicates
Author: syounkin
Created: 2012-01-25 16:21:41+00:00
State: open

Right now motherPhenoData, and presumably fatherPhenoData and offspringPhenoData list the dummy sampleNames that account for trios with the same parents. For example,

> motherPhenoData(pitt.trioSetList)
An object of class "AnnotatedDataFrame"
sampleNames: 175095398 175071365 ... 175136465___DUP1 (752 total)
varLabels: Sample.Name ID ... SentrixPosition (7 total)
varMetadata: labelDescription

Note the ___DUP1.

Do we want to do this, or do we want to list distinct sampleNames? The total of 752 is misleading, as there are only 494 mothers in this pedigree.

> length(unique(motherNames(pitt.pedigree)))
[1] 494
> length(motherNames(pitt.pedigree))
[1] 752
>

Note that we may want to address this for the methods motherNames, fatherNames and offspringNames.