SnapATAC
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RunDiffusionMaps fails with pmat
I'm trying to do dimensionality reduction using the pmat
instead of bmat
. However, the trainRegression
function has the bmat
hardcoded, which causes RunDiffusionMaps
to fail.
https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/utilities.R#L125-L126
There is also a typo here in runDiffusionMapsExtension
:
https://github.com/r3fang/SnapATAC/blob/c3ab177558f0fe9c47cbd68969df7b06de5b07d9/R/runLDM.R#L222-L223
Hi, I face a similar issue when I try to run RunDiffusionMaps with pmat instead of bmat. Here is the error I get (at the trainRegression function) :
Epoch: checking the inputs ... Epoch: computing jaccard similarity matrix ... Epoch: fitting regression model ... Error in density.default(x = row.covs, bw = "nrd", adjust = 1) : need at least 2 points to select a bandwidth automatically
I met the same error, how can I solve this problem? please help me
I've pushed some fixes here https://github.com/kundajelab/SnapATAC/tree/4cb43f7, you can try this version.
I've pushed some fixes here https://github.com/kundajelab/SnapATAC/tree/4cb43f7, you can try this version.
I follow your advice trying this version, but there is still the same error.
Did you reinstall SnapATAC using the version I linked? You will have to uninstall the correct version and run install from the above link.
Did you reinstall SnapATAC using the version I linked? You will have to uninstall the correct version and run install from the above link.
yes, I did that
Hard to say then. Perhaps you can insert some print statements around this line
row.covs.dens <- density(x = row.covs, bw = 'nrd', adjust = 1)
in the trainRegression.R
function in utilities.R
and see where it's bugging out.
Also looks like there's a SnapATAC2 version out now https://github.com/kaizhang/SnapATAC2.
Hard to say then. Perhaps you can insert some print statements around this line
row.covs.dens <- density(x = row.covs, bw = 'nrd', adjust = 1)
in thetrainRegression.R
function inutilities.R
and see where it's bugging out.Also looks like there's a SnapATAC2 version out now https://github.com/kaizhang/SnapATAC2.
thank you very much. Could you tell there is the link to the SnapATAC2's source paper is?
Not sure, looks like it's in development
Not sure, looks like it's in development
Okay, thank you for your reply and help