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smgogarten
reviewed
Oct 4, 2021
| BPPARAM=bpparam(), verbose=TRUE) { | ||
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| # better way to handle these checks? | ||
| if(class(gdsobj) == 'SeqVarBlockIterator' && score.cov){ |
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should be if(is(gdsobj, "SeqVarBlockIterator") && score.cov)
Instead of having a separate score.cov logical argument, select whether to return covariance matrices by input object type. A block iterator is used for single variant tests, so only return Score and Score.SE (no covariance) for SeqVarBlockIterator objects.
…; will need separate method
smgogarten
reviewed
Oct 14, 2021
| chr=getChromosome(gdsobj, char=TRUE), | ||
| pos=getPosition(gdsobj), | ||
| stringsAsFactors=FALSE) | ||
| if (alleles) { |
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I just made a change in GWASTools so this should work now (allele columns were missing previously)
Names for group IDs in SeqVarListIterator objects may be taken from the names of the GRangesList object defining iterations. If that is NULL, it is not straightforward to construct names since variants in each group are not sequential nor even required to be on the same chromosome. Instead, number groups with sequential integers.
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