Conversion to SingleCellExperiment from Seurat objects
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@wolfgang-huber-3550
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EMBL European Molecular Biology Laborat…

I realize this is slightly out of scope since Seurat 2.3 is on CRAN, not Bioconductor, but given its developers recent interactions with the SIngleCellExperiment developers, I hope it's OK to post this here:

 

When trying to convert one of the Seurat data objects from the tabula muris, I get the following error. This seems to be related to the fact that the raw.data slot in this particular object is stored as a data.frame (rather than, say, matrix or dgCMatrix), which confuses the SummarizedExperiment constructor. A workaround is to convert the slot to a regular matrix before the conversion (see below). Perhaps it'd be a good idea to add that kind of workaround to the Seurat::as.SingleCellExperiment.seurat function (an alternative would be to clean the internet from legacy Seurat objects, which is perhaps less realistic?)

library("Seurat")

# from https://figshare.com/articles/Robject_files_for_tissues_processed_by_Seurat/5821263
load("facs_Liver_seurat_tiss.Robj")
tiss2 = tiss
tiss2@raw.data = as.matrix(tiss2@raw.data)

sc2 = as.SingleCellExperiment(tiss2)
sc  = as.SingleCellExperiment(tiss)

#Error in seq_len(ncol(assay)) :
#  argument must be coercible to non-negative integer
#In addition: Warning message:
#In seq_len(ncol(assay)) : first element used of 'length.out' argument

> devtools::session_info()
Session info ------------------------------------------------------------------
 setting  value
 version  R Under development (unstable) (2018-05-18 r74745)
 system   x86_64, darwin17.5.0
 ui       unknown
 language (EN)
 collate  en_US.UTF-8
 tz       Europe/Berlin
 date     2018-05-21

Packages ----------------------------------------------------------------------
 package              * version    date       source
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 ape                    5.1        2018-04-04 CRAN (R 3.6.0)
 assertthat             0.2.0      2017-04-11 CRAN (R 3.6.0)
 backports              1.1.2      2017-12-13 CRAN (R 3.6.0)
 base                 * 3.6.0      2018-05-19 local
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 codetools              0.2-15     2016-10-05 CRAN (R 3.6.0)
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 datasets             * 3.6.0      2018-05-19 local
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 Formula                1.2-3      2018-05-03 CRAN (R 3.6.0)
 fortunes             * 1.5-4      2016-12-29 CRAN (R 3.6.0)
 fpc                    2.1-11     2018-01-13 CRAN (R 3.6.0)
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 GenomeInfoDb           1.17.1     2018-05-21 Bioconductor
 GenomeInfoDbData       1.1.0      2018-05-19 Bioconductor
 GenomicRanges          1.33.5     2018-05-21 Bioconductor
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 gower                  0.1.2      2017-02-23 CRAN (R 3.6.0)
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 gtools                 3.5.0      2015-05-29 CRAN (R 3.6.0)
 Hmisc                  4.1-1      2018-01-03 CRAN (R 3.6.0)
 htmlTable              1.11.2     2018-01-20 CRAN (R 3.6.0)
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 magic                  1.5-8      2018-01-26 CRAN (R 3.6.0)
 magrittr               1.5        2014-11-22 CRAN (R 3.6.0)
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 pillar                 1.2.2      2018-04-26 CRAN (R 3.6.0)
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 plyr                   1.8.4      2016-06-08 CRAN (R 3.6.0)
 png                    0.1-7      2013-12-03 CRAN (R 3.6.0)
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 prodlim                2018.04.18 2018-04-18 CRAN (R 3.6.0)
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 psych                  1.8.4      2018-05-06 CRAN (R 3.6.0)
 purrr                  0.2.4      2017-10-18 CRAN (R 3.6.0)
 R.methodsS3            1.7.1      2016-02-16 CRAN (R 3.6.0)
 R.oo                   1.22.0     2018-04-22 CRAN (R 3.6.0)
 R.utils                2.6.0      2017-11-05 CRAN (R 3.6.0)
 R6                     2.2.2      2017-06-17 CRAN (R 3.6.0)
 ranger                 0.9.0      2018-01-09 CRAN (R 3.6.0)
 RANN                   2.5.1      2017-05-21 CRAN (R 3.6.0)
 RColorBrewer           1.1-2      2014-12-07 CRAN (R 3.6.0)
 Rcpp                   0.12.17    2018-05-18 CRAN (R 3.6.0)
 RcppRoll               0.2.2      2015-04-05 CRAN (R 3.6.0)
 RCurl                  1.95-4.10  2018-01-04 CRAN (R 3.6.0)
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 ROCR                   1.0-7      2015-03-26 CRAN (R 3.6.0)
 rpart                  4.1-13     2018-02-23 CRAN (R 3.6.0)
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 scales                 0.5.0      2017-08-24 CRAN (R 3.6.0)
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 SDMTools               1.1-221    2014-08-05 CRAN (R 3.6.0)
 segmented              0.5-3.0    2017-11-30 CRAN (R 3.6.0)
 Seurat               * 2.3.1      2018-05-05 CRAN (R 3.6.0)
 sfsmisc                1.1-2      2018-03-05 CRAN (R 3.6.0)
 SingleCellExperiment   1.3.2      2018-05-21 Bioconductor
 sn                     1.5-2      2018-04-24 CRAN (R 3.6.0)
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 splines                3.6.0      2018-05-19 local
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 stringi                1.2.2      2018-05-02 CRAN (R 3.6.0)
 stringr                1.3.1      2018-05-10 CRAN (R 3.6.0)
 SummarizedExperiment   1.11.3     2018-05-21 Bioconductor
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Seurat SingleCellExperiment • 1.7k views
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