search

hansenlab / bsseq

Devel repository for bsseq
36 stars 26 forks source link

Don't checkDimnames when making SummarizedExperiment #113

Open jamespeapen opened 2 years ago

jamespeapen commented 2 years ago

We've been getting this error when using bsseq::combine on bsseq objects with different colnames:

Error in SummarizedExperiment(assays = ans_assays,rowRanges = ans_rowRanges,: 
the rownames and colnames of the supplied assay(s) must be NULL or 
identical to those of the RangedSummarizedExperiment object (or derivative) to construct

This patch remvoves the validity check so that the SummarizedExperiment object is created without error.

PeteHaitch commented 2 years ago

@jamespeapen can you please share a reprex that illustrates the problem.

jamespeapen commented 2 years ago

https://github.com/jamespeapen/biscuiteer/blob/bsseq/bslist.rds?raw=true

bs_list <- readRDS("bslist.rds")
myBS <- bs_list[[1]]
for (i in (2:length(bs_list))) {
  myBS <- bsseq::combine(myBS, bs_list[[i]])
}
PeteHaitch commented 2 years ago

Sorry, I've been very busy and haven't had time to consider this, yet. @kasperdanielhansen what do you think?