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hansenlab / minfi

Devel repository for minfi
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Fix addSex and plotSex #136

Closed markgene closed 6 years ago

markgene commented 6 years ago

plotSex() returned an error message Error: all(c("predictedSex", "xMed", "yMed") %in% names(object)) is not TRUE when running with the examples, where addSex() returned GMsetEx using minfiData example data. It is because the addSex() only adds predictedSex column but not xMed or yMed. I fix addSex().

Another bug is the check point of names(object). As the object is [Genomic]MethylSet, we should use colnames(pData(object)).

PeteHaitch commented 6 years ago

Thans, Mark. minfi is undergoing some pretty substantial internal changes prior to the next release. I'll be sure to incorporate your patch (or similar) into these changes.

PeteHaitch commented 6 years ago

I've addressed this in https://github.com/PeteHaitch/minfi/commit/adbce4467b7efd9a30bffaf530505ef0ce4719fe, which will soon be merged into the version of minfi available from Bioconductor.

Thanks again for the report.

markgene commented 6 years ago

Thank you, Peter!