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
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