error in gap statistic

[timydaley]

Error in distMatrix[medoid, which(cluster == medoid)] :
subscript out of bounds

@linzx06 : do you know what this means? What can I do to debug the issue? The data is from the Buenrostro hematopoietic scATAC-seq data. I can send it to you if that'll help.

[linzx06]

Sure, please send it to me.

…

On Wed, Aug 22, 2018 at 7:30 AM, Timothy Daley ***@***.***> wrote: Error in distMatrix[medoid, which(cluster == medoid)] : subscript out of bounds @linzx06 <https://github.com/linzx06> : do you know what this means? What can I do to debug the issue? The data is from the Buenrostro hematopoietic scATAC-seq data. I can send it to you if that'll help. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALQrSYU8Q9W3_InN3ssSqOcEAqHBTYUjks5uTJgjgaJpZM4WGwTU> .

[timydaley]

Timothy Patrick Daley has shared OneDrive for Business files with you. To view them, click the links below. <https://office365stanford-my.sharepoint.com/:t:/g/personal/tdaley_stanford_edu/EYhMbxfDQ91Gs_Bef8lR2uUBz_0qAxpXikrGDwXb-5xlYA> [https://r1.res.office365.com/owa/prem/images/dc-txt_20.png]<https://office365stanford-my.sharepoint.com/:t:/g/personal/tdaley_stanford_edu/EYhMbxfDQ91Gs_Bef8lR2uUBz_0qAxpXikrGDwXb-5xlYA> cellNames2.txt<https://office365stanford-my.sharepoint.com/:t:/g/personal/tdaley_stanford_edu/EYhMbxfDQ91Gs_Bef8lR2uUBz_0qAxpXikrGDwXb-5xlYA> <https://office365stanford-my.sharepoint.com/:u:/g/personal/tdaley_stanford_edu/EWHFvxm-c6NFqTamrPHGj90BQ5utIPdsnkipw_ZTRpBWsw> [https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]<https://office365stanford-my.sharepoint.com/:u:/g/personal/tdaley_stanford_edu/EWHFvxm-c6NFqTamrPHGj90BQ5utIPdsnkipw_ZTRpBWsw> scATACseq_counts2.txt.bz2<https://office365stanford-my.sharepoint.com/:u:/g/personal/tdaley_stanford_edu/EWHFvxm-c6NFqTamrPHGj90BQ5utIPdsnkipw_ZTRpBWsw> The matrices are attached. The code to load and run gap stat is given below. scATACseqCounts = as.matrix(Matrix::readMM("scATACseq_counts2.txt")) cellNames = scan("cellNames2.txt", what = "chraracter()") colnames(scATACseqCounts) = cellNames weights = apply(scATACseqCounts + 0.001, 2, mean) scATACseqCountsGapStat = getGapStat(scATACseqCounts, weights, nClusters = 1:30, nPerm = 30, nTop = 5000, quiet = FALSE) It gets to 10% and then the error appears. Thanks Zhixiang. Timothy Daley Stanford University, Departments of Statistics and Bioengineering.

________________________________ From: linzx06 <[email protected]> Sent: Tuesday, August 21, 2018 5:15:29 PM To: SUwonglab/scABC Cc: Timothy Patrick Daley; Author Subject: Re: [SUwonglab/scABC] error in gap statistic (#5) Sure, please send it to me.

On Wed, Aug 22, 2018 at 7:30 AM, Timothy Daley ***@***.***> wrote: Error in distMatrix[medoid, which(cluster == medoid)] : subscript out of bounds @linzx06 <https://github.com/linzx06> : do you know what this means? What can I do to debug the issue? The data is from the Buenrostro hematopoietic scATAC-seq data. I can send it to you if that'll help. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#5>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ALQrSYU8Q9W3_InN3ssSqOcEAqHBTYUjks5uTJgjgaJpZM4WGwTU> .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#5 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AHBhcq8xoefBK8ADuSPlBEGYLp0ivo3yks5uTKKhgaJpZM4WGwTU>.

[MahdiZ11]

Hi guys, is this fixed?