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colomemaria / epiAneufinder

R package to detect breakpoints and assign somies to scATAC-seq data
GNU General Public License v3.0
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calling copy numbers using only counts matrix #16

Closed Katherine-Kelly closed 8 months ago

Katherine-Kelly commented 11 months ago

I am using some public data where fragments files are not available - is it possible to run epiAneufinder using only a counts matrix or is the fragments file required?

thek71 commented 11 months ago

Thank you for the message. Currently epiAneufinder takes as input only bam or fragment files. But we can add a function include count matrix input. Can you please tell us what kind of count matrix you have (bins, peaks?).

Katherine-Kelly commented 10 months ago

Thanks, that would be very helpful - I would be working with a peak counts matrix.

Abdul-Moeed commented 9 months ago

Hi! Any updates on this?

thek71 commented 9 months ago

Hi, we have created a new function that uses as input a count matrix and we are currently testing the performance, since we have an even more sparse matrix as input. We plan to release it next week. I will keep you posted in this thread.

thek71 commented 9 months ago

Hi all, in the dev branch is a new implementation that takes as input also a count matrix. The input should be in 10X format (3 files, the barcodes.tsv, peaks.bed and matrix.mtx with this naming for now). We compared the results of CNV calling with the peak matrix compared to fragment file as input. We used the SNU601 dataset as in the publication and compared with the scWGS dataset as groundtruth. The correlation between the CNVs is worse when using the matrix as input (0.74 from 0.85). We loose reads that are not in peak regions so overall we get less coverage over the genome. The result is that we can miss some gains and losses that would otherwise have been identified with the fragment input. So we would suggest a bit of caution in the interpretation of the results, but as you can see from the comparison with the groundtruth the method still gives valid results. Try it out and please give us any feedback that you have. We will push it in the main branch in a couple of days, when we finalize the vignette.

Best, Katia and Katharina

Abdul-Moeed commented 8 months ago

Nice, I tested and it works. Thanks!

thek71 commented 8 months ago

The code has been merged to the main branch. I am closing the issue, since everything seems to be in order.