Error in if ((3 * a[b + c]) < a[b]) { : argument is of length zero #14
Description
Hi,
I run CIDR with a 32738 gene x 6143 cell dataset.
This is the main code, however, when running the last step (scCluster(sdata)), the function returns an error message "argument is of length zero".
Could you help me figure out the problem and fix it?
>dat <- counts(sce)
>sdata <- scDataConstructor(dat)
>sdata <- determineDropoutCandidates(sdata)
>sdata <- wThreshold(sdata)
>sdata <- scDissim(sdata, threads = params$nCore)
>sdata <- scPCA(sdata, plotPC =F)
>sdata <- nPC(sdata)
>sdata <- scCluster(sdata)
Error in if ((3 * a[b + c]) < a[b]) { : argument is of length zero
Here is the data structure of sdata.
> str(sdata)
Formal class 'scData' [package "cidr"] with 20 slots
..@ tags : num [1:20751, 1:6143] 0 0 0 0 0 0 0 0 0 0 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:20751] "ENSG00000228463" "ENSG00000228327" "ENSG00000237491" "ENSG00000225880" ...
.. .. ..$ : chr [1:6143] "AAACATACACTGGT-1" "AAACATACAGACTC-1" "AAACATTGACCAAC-1" "AAACATTGAGGCGA-1" ...
..@ tagType : chr "raw"
..@ sampleSize : int 6143
..@ librarySizes : Named num [1:6143] 19337 8786 24636 16030 27341 ...
.. ..- attr(*, "names")= chr [1:6143] "AAACATACACTGGT-1" "AAACATACAGACTC-1" "AAACATTGACCAAC-1" "AAACATTGAGGCGA-1" ...
..@ nData : num [1:20751, 1:6143] 0 0 0 0 0 0 0 0 0 0 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:20751] "ENSG00000228463" "ENSG00000228327" "ENSG00000237491" "ENSG00000225880" ...
.. .. ..$ : chr [1:6143] "AAACATACACTGGT-1" "AAACATACAGACTC-1" "AAACATTGACCAAC-1" "AAACATTGAGGCGA-1" ...
..@ priorTPM : num 1
..@ dThreshold : num [1:6143] 8.62 8.62 8.62 8.62 8.62 ...
..@ wThreshold : Named num 9.6
.. ..- attr(*, "names")= chr "a"
..@ pDropoutCoefA : Named num 4.31
.. ..- attr(*, "names")= chr "a"
..@ pDropoutCoefB : Named num 9.6
.. ..- attr(*, "names")= chr "b"
..@ dropoutCandidates: logi [1:20751, 1:6143] TRUE TRUE TRUE TRUE TRUE TRUE ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : chr [1:20751] "ENSG00000228463" "ENSG00000228327" "ENSG00000237491" "ENSG00000225880" ...
.. .. ..$ : chr [1:6143] "AAACATACACTGGT-1" "AAACATACAGACTC-1" "AAACATTGACCAAC-1" "AAACATTGAGGCGA-1" ...
..@ PC : num [1:6143, 1:3353] 16.3 20.7 18.3 17.8 14.2 ...
.. ..- attr(*, "dimnames")=List of 2
.. .. ..$ : NULL
.. .. ..$ : chr [1:3353] "Axis.1" "Axis.2" "Axis.3" "Axis.4" ...
..@ variation : num [1:3353] 0.20404 0.01935 0.01156 0.01042 0.00794 ...
..@ eigenvalues : num [1:6143] 1849685 175401 104792 94445 71980 ...
..@ dissim : num [1:6143, 1:6143] 0 19.1 18 13.2 17.8 ...
..@ nCluster : num 0
..@ clusters : logi(0)
..@ nPC : num 4
..@ cMethod : chr(0)
..@ correction : chr "none"