Currently buildSubclones() requires both a (pure) tumor and its matched normal, in order for mixSubclones() to perform a mixture. This makes it impossible to use this function with one of the acnr data set: GSE29172_H1395, because we do not have a 0% dilution for that one.
Couldn't we resample from a normal region (from the tumor) in order to emulate a matched normal?
It seems to me that we could. We need to make sure that the genotypes match, but this is already done in buildSubclone.
Currently
buildSubclones()requires both a (pure) tumor and its matched normal, in order for mixSubclones() to perform a mixture. This makes it impossible to use this function with one of theacnrdata set: GSE29172_H1395, because we do not have a 0% dilution for that one.Couldn't we resample from a normal region (from the tumor) in order to emulate a matched normal?
It seems to me that we could. We need to make sure that the genotypes match, but this is already done in
buildSubclone.