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Question: GenomicRanges_RaggedExperiment Error in as background, class mcol no method or default for coercing logical to factor
0
gravatar for Taran
28 days ago by
Taran0
Taran0 wrote:

Hi,

I have a total of 124 samples (each of them a GRanges objetct) in a list.

transfor[1]
$EPR000148
GRanges object with 57 ranges and 1 metadata column:
       seqnames                 ranges strand |     score
          <Rle>              <IRanges>  <Rle> | <integer>
   [1]     chr1 [   129285,   6314822]      * |         1
   [2]     chr1 [ 12855876,  13802437]      * |         1
   [3]     chr1 [ 16344494,  33282775]      * |         1
   [4]     chr1 [117622286, 148951207]      * |         1
   [5]     chr2 [ 90464785,  95963242]      * |         1
   ...      ...                    ...    ... .       ...
  [53]    chr21   [10907208, 14756481]      * |         0
  [54]    chr21   [44837551, 47552385]      * |         1
  [55]    chr22   [18304392, 18900750]      * |         1
  [56]    chr22   [21045398, 21742598]      * |         1
  [57]    chr22   [42523409, 42779699]      * |         1
 -------
  seqinfo: 20 sequences from an unspecified genome; no seqlength

I get the following warning:

Warning message:
In `[<-`(`*tmp*`, i, value = <S4 object of class structure("GRanges", package = "GenomicRanges")>) :
  implicit list embedding of S4 objects is deprecated

Performing the function RaggedExperiment works perfect.

>ragedtransfor<-RaggedExperiment(transfor, colData=colDat)

> ragedtransfor
class: RaggedExperiment
dim: 3828 124
assays(1): score
rownames: NULL
colnames(124): EPR000148 EPR002842 ... EPR985377 EPR990968
colData names(1): id

but when performing any of the Assayfunctions, I get the following:

sparseAssay(ragedtransfor)
Error in as(background, class(mcol)) :
  no method or default for coercing “logical” to “factor”

I performed the debug option and it crashes in the following step:

debug: dimnames[[1]] <- as.character(.rowRanges(x))
Browse[2]>
debug: na <- as(background, class(mcol))
Browse[2]>
Error in as(background, class(mcol)) :
  no method or default for coercing “logical” to “factor”

My sessionInfo():

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /home/.../homews/R342/lib64/R/lib/libRblas.so
LAPACK: /home/.../homews/R342/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] RaggedExperiment_1.2.0 GenomicRanges_1.30.0   GenomeInfoDb_1.14.0
[4] IRanges_2.12.0         S4Vectors_0.16.0       BiocGenerics_0.24.0
[7] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] lattice_0.20-35            matrixStats_0.52.2
 [3] bitops_1.0-6               grid_3.4.2
 [5] zlibbioc_1.24.0            XVector_0.18.0
 [7] Matrix_1.2-11              tools_3.4.2
 [9] Biobase_2.38.0             RCurl_1.95-4.8
[11] DelayedArray_0.4.1         compiler_3.4.2
[13] SummarizedExperiment_1.8.0 GenomeInfoDbData_0.99.1

I attach a subset of the data so that anyone can reproduce the error.

https://www.dropbox.com/sh/wmb4ibdigzegnw4/AAAJA_z1nBpB9ppZrEWOPkQba?dl=0

ADD COMMENTlink modified 23 days ago by Marcel Ramos ♦♦ 90 • written 28 days ago by Taran0

Hi Taran, 

Thank you for your report. I wasn't able to get to it yesterday. I will have a look at it today. 

Regards,

Marcel

ADD REPLYlink written 26 days ago by Marcel Ramos ♦♦ 90
1
gravatar for Marcel Ramos
23 days ago by
Marcel Ramos ♦♦ 90
United States
Marcel Ramos ♦♦ 90 wrote:

Hi Taran, 

Apologies for the late response. I have looked at the issue and we're working on a fix. 
The reason you're getting an error in that call is that you are introducing an "score" column
of type `factor`. 
The quick fix for this issue is to coerce the "score" column to character and rerun the call.

We are currently working on a fix for this. Thanks for reporting this. 

 

Best regards,

Marcel

ADD COMMENTlink written 23 days ago by Marcel Ramos ♦♦ 90
1

Updates: This has been fixed in `1.2.3` in release and `1.3.5` in devel. 

Marcel

ADD REPLYlink modified 23 days ago • written 23 days ago by Marcel Ramos ♦♦ 90
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