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ChenFengling / RHiCDB

detect and visualize contact domain boundaries (CDBs) or differential CDBs from Hi-C (R version)
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failure in writing CDB outputs: Error in FUN(newX[, i], ...) : invalid 'type' (list) of argument #1

Open yenagra opened 6 years ago

yenagra commented 6 years ago

Hi. I tried to run a set of data in sparse format containing only one chromosome, however it failed and the message goes:

[1] "One sample is provided, detect CDBs!" [1] " Detect all local maximum peaks on each chromosome." [1] "Processing chr1" Your input matrix is normalized matrix, skip KR normalization find local maximum [1] " " [1] " Write outputs: localmax.txt." [1] " " [1] " Decide cut off using enrichmentscore. Write outputs:EScurve.png." [1] " Annotate CDBs with CDB conservation. Write outputs:CDB.txt." [1] "CDB.txt format:#chr start end LRI avgRI conserve_or_not" Error in FUN(newX[, i], ...) : invalid 'type' (list) of argument

later I tried in dense format but also failed when writing CDB outputs, with the same message

Error in FUN(newX[, i], ...) : invalid 'type' (list) of argument

However, it worked well with the sample data, and I couldn't find the reason.

ChenFengling commented 6 years ago

Thanks for your interest in the HiCDB. We didn't recommend to run on single chromosome before because we found the cutoff chosen is more stable when working on the whole genome . However, as this question was also asked by other people, a new version is coming soon. And if we made the change, we will inform you by email at once ! Now, you can run it on the whole genome if possible.

yenagra commented 6 years ago

Okay, thank you.

fchen notifications@github.com 于2018年9月25日周二 下午11:09写道：

Thanks for your interest in the HiCDB. We didn't recommend to run on single chromosome before because we found the cutoff chosen is more stable when working on the whole genome . However, as this question was also asked by other people, a new version is coming soon. And if we made the change, we will inform you by email at once ! Now, you can run it on the whole genome if possible.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ChenFengling/RHiCDB/issues/1#issuecomment-424380864, or mute the thread https://github.com/notifications/unsubscribe-auth/AX_bqbtIKt3dVZQSb4wXCFV9tguIzf3Tks5uekcggaJpZM4W4Hzp .