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stephaniehicks / methylCC

R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms
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Error in `colnames<-`(`*tmp*`, value = cell_levels) : attempt to set 'colnames' on an object with less than two dimensions #7

Closed xxz1482 closed 1 year ago

xxz1482 commented 1 year ago

Hi, An issue with estimatecc{methylCC} that I encountered while running with my BSseq object.

est <- estimatecc(BSseq_obj, include_dmrs = FALSE) Error in colnames<-(*tmp*, value = cell_levels) : attempt to set 'colnames' on an object with less than two dimensions

Any comments or suggestions are truly appreciated! Lastly, once we get the cell compositions, could methylCC do cell-specific adjustment on the original WGBS data and return an adjusted WGBS data? Thanks very much in advance!

stephaniehicks commented 1 year ago

Hi, is there a small reprex (reproducible example) (https://reprex.tidyverse.org/) you could provide to help me debug the issue? Thanks!

xxz1482 commented 1 year ago

Hi Dr. Hicks,

Attached, I include an example WGBS data that I used to generate my BSseq object.

TotalReads.txt MethylReads.txt

stephaniehicks commented 1 year ago

Could you also provide the code you are using? Thanks!

xxz1482 commented 1 year ago

Thanks very much for your helps! Rcode.txt

stephaniehicks commented 1 year ago

Hi,

I am still not sure about the colnames issue. However, this package only estimates the cell composition. It does not return any normalized / adjusted data. Thanks!