Contents

1 Convert between DESeqDataSet and DGEList objects

The following examples demonstrate how to shuttle data between DESeqDataSet and DGEList containers. Before we start, let’s first load the required packages.

library(DESeq2)
library(edgeR)
library(DEFormats)

1.1 DGEList to DESeqDataSet

We will illustrate the functionality of the package on a mock expression data set of an RNA-seq experiment. The sample counts table can be generated using the function provided by DEFormats:

counts = simulateRnaSeqData()

The resulting object is a matrix with rows corresponding to genomic features and columns to samples.

head(counts)
##       sample1 sample2 sample3 sample4 sample5 sample6
## gene1      85      76     103     107     140     124
## gene2       1       6      11       6       1       4
## gene3      80      98      39      82      97     113
## gene4      92      83      59      85     100      98
## gene5      36      24      18      50      22      15
## gene6       0       0       1       4       2       3

In order to construct a DGEList object we need to provide, apart from the counts matrix, the sample grouping.

group = rep(c("A", "B"), each = 3)

dge = DGEList(counts, group = group)
dge
## An object of class "DGEList"
## $counts
##       sample1 sample2 sample3 sample4 sample5 sample6
## gene1      85      76     103     107     140     124
## gene2       1       6      11       6       1       4
## gene3      80      98      39      82      97     113
## gene4      92      83      59      85     100      98
## gene5      36      24      18      50      22      15
## 995 more rows ...
## 
## $samples
##         group lib.size norm.factors
## sample1     A    42832            1
## sample2     A    40511            1
## sample3     A    39299            1
## sample4     B    43451            1
## sample5     B    40613            1
## sample6     B    43662            1

A DGEList object can be easily converted to a DESeqDataSet object with the help of the function as.DESeqDataSet.

dds = as.DESeqDataSet(dge)
dds
## class: DESeqDataSet 
## dim: 1000 6 
## metadata(1): version
## assays(1): counts
## rownames(1000): gene1 gene2 ... gene999 gene1000
## rowData names(0):
## colnames(6): sample1 sample2 ... sample5 sample6
## colData names(3): group lib.size norm.factors

Just to make sure that the coercions conserve the data and metadata, we now convert dds back to a DGEList and compare the result to the original dge object.

identical(dge, as.DGEList(dds))
## [1] TRUE

Note that because of the use of reference classes in the SummarizedExperiment class which DESeqDataSet extends, identical will return FALSE for any two DESeqDataSet instances, even for ones constructed from the same input:

dds1 = DESeqDataSetFromMatrix(counts, data.frame(condition=group), ~ condition)
dds2 = DESeqDataSetFromMatrix(counts, data.frame(condition=group), ~ condition)

identical(dds1, dds2)
## [1] FALSE

1.2 DESeqDataSet to DGEList

Instead of a count matrix, simulateRnaSeqData can also return an annotated RangedSummarizedExperiment object. The advantage of such an object is that, apart from the counts matrix stored in the assay slot, it also contains sample description in colData, and gene information stored in rowRanges as a GRanges object.

se = simulateRnaSeqData(output = "RangedSummarizedExperiment")
se
## class: RangedSummarizedExperiment 
## dim: 1000 6 
## metadata(1): version
## assays(1): counts
## rownames(1000): gene1 gene2 ... gene999 gene1000
## rowData names(3): trueIntercept trueBeta trueDisp
## colnames(6): sample1 sample2 ... sample5 sample6
## colData names(1): condition

The se object can be readily used to construct a DESeqDataSet object,

dds = DESeqDataSet(se, design = ~ condition)

which can be converted to a DGEList using the familiar method.

dge = as.DGEList(dds)
dge
## An object of class "DGEList"
## $counts
##       sample1 sample2 sample3 sample4 sample5 sample6
## gene1      85      76     103     107     140     124
## gene2       1       6      11       6       1       4
## gene3      80      98      39      82      97     113
## gene4      92      83      59      85     100      98
## gene5      36      24      18      50      22      15
## 995 more rows ...
## 
## $samples
##         group lib.size norm.factors
## sample1     A    42832            1
## sample2     A    40511            1
## sample3     A    39299            1
## sample4     B    43451            1
## sample5     B    40613            1
## sample6     B    43662            1
## 
## $genes
##       seqnames start end width strand trueIntercept trueBeta  trueDisp
## gene1        1     1 100   100      *      6.525909        0 0.1434076
## gene2        1   101 200   100      *      3.347533        0 0.4929634
## gene3        1   201 300   100      *      6.659599        0 0.1395659
## gene4        1   301 400   100      *      6.544859        0 0.1428412
## gene5        1   401 500   100      *      4.829283        0 0.2407022
## 995 more rows ...

Note the additional genes element on the dge list compared to the object from the previous section.

2 Create DGEList objects from SummarizedExperiment

Similarly as for the DESeqDataSet constructor from DESeq2, it is possible to directly use RangedSummarizedExperiment objects as input to the generic DGEList constructor defined in DEFormats. This allows you to use common input objects regardless of whether you are applying DESeq2 or edgeR to perform your analysis, or to easily switch between these two tools in your pipeline.

names(colData(se)) = "group"
dge = DGEList(se)
dge
## An object of class "DGEList"
## $counts
##       sample1 sample2 sample3 sample4 sample5 sample6
## gene1      85      76     103     107     140     124
## gene2       1       6      11       6       1       4
## gene3      80      98      39      82      97     113
## gene4      92      83      59      85     100      98
## gene5      36      24      18      50      22      15
## 995 more rows ...
## 
## $samples
##         group lib.size norm.factors
## sample1     A    42832            1
## sample2     A    40511            1
## sample3     A    39299            1
## sample4     B    43451            1
## sample5     B    40613            1
## sample6     B    43662            1
## 
## $genes
##       seqnames start end width strand trueIntercept trueBeta  trueDisp
## gene1        1     1 100   100      *      6.525909        0 0.1434076
## gene2        1   101 200   100      *      3.347533        0 0.4929634
## gene3        1   201 300   100      *      6.659599        0 0.1395659
## gene4        1   301 400   100      *      6.544859        0 0.1428412
## gene5        1   401 500   100      *      4.829283        0 0.2407022
## 995 more rows ...

We renamed the condition column of colData(se) to group in order to allow edgeR to automatically pick up the correct sample grouping. Another way of specifying this is through the argument group to DGEList.

3 FAQ

3.1 Coerce DGEList to RangedSummarizedExperiment

Even though there is no direct method to go from a DGEList to a RangedSummarizedExperiment, the coercion can be easily performed by first converting the object to a DESeqDataSet, which is a subclass of RangedSummarizedExperiment, and then coercing the resulting object to its superclass.

dds = as.DESeqDataSet(dge)
rse = as(dds, "RangedSummarizedExperiment")
rse
## class: RangedSummarizedExperiment 
## dim: 1000 6 
## metadata(1): version
## assays(1): counts
## rownames(1000): gene1 gene2 ... gene999 gene1000
## rowData names(3): trueIntercept trueBeta trueDisp
## colnames(6): sample1 sample2 ... sample5 sample6
## colData names(3): group lib.size norm.factors

4 Session info

sessionInfo()
## R Under development (unstable) (2018-11-17 r75624)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.1 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.9-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.9-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] DEFormats_1.11.1            edgeR_3.25.3               
##  [3] limma_3.39.3                DESeq2_1.23.3              
##  [5] SummarizedExperiment_1.13.0 DelayedArray_0.9.5         
##  [7] BiocParallel_1.17.5         matrixStats_0.54.0         
##  [9] Biobase_2.43.0              GenomicRanges_1.35.1       
## [11] GenomeInfoDb_1.19.1         IRanges_2.17.4             
## [13] S4Vectors_0.21.9            BiocGenerics_0.29.1        
## [15] BiocStyle_2.11.0           
## 
## loaded via a namespace (and not attached):
##  [1] bit64_0.9-7            splines_3.6.0          Formula_1.2-3         
##  [4] assertthat_0.2.0       BiocManager_1.30.4     latticeExtra_0.6-28   
##  [7] blob_1.1.1             GenomeInfoDbData_1.2.0 yaml_2.2.0            
## [10] RSQLite_2.1.1          pillar_1.3.1           backports_1.1.3       
## [13] lattice_0.20-38        glue_1.3.0             digest_0.6.18         
## [16] RColorBrewer_1.1-2     XVector_0.23.0         checkmate_1.8.5       
## [19] colorspace_1.3-2       htmltools_0.3.6        Matrix_1.2-15         
## [22] plyr_1.8.4             XML_3.98-1.16          pkgconfig_2.0.2       
## [25] genefilter_1.65.0      bookdown_0.9           zlibbioc_1.29.0       
## [28] purrr_0.2.5            xtable_1.8-3           scales_1.0.0          
## [31] tibble_2.0.0           htmlTable_1.13         annotate_1.61.0       
## [34] ggplot2_3.1.0          nnet_7.3-12            lazyeval_0.2.1        
## [37] survival_2.43-3        magrittr_1.5           crayon_1.3.4          
## [40] memoise_1.1.0          evaluate_0.12          foreign_0.8-71        
## [43] tools_3.6.0            data.table_1.11.8      stringr_1.3.1         
## [46] locfit_1.5-9.1         munsell_0.5.0          cluster_2.0.7-1       
## [49] AnnotationDbi_1.45.0   bindrcpp_0.2.2         compiler_3.6.0        
## [52] rlang_0.3.0.1          grid_3.6.0             RCurl_1.95-4.11       
## [55] rstudioapi_0.8         htmlwidgets_1.3        bitops_1.0-6          
## [58] base64enc_0.1-3        rmarkdown_1.11         gtable_0.2.0          
## [61] DBI_1.0.0              R6_2.3.0               gridExtra_2.3         
## [64] knitr_1.21             dplyr_0.7.8            bit_1.1-14            
## [67] bindr_0.1.1            Hmisc_4.1-1            stringi_1.2.4         
## [70] Rcpp_1.0.0             geneplotter_1.61.0     rpart_4.1-13          
## [73] acepack_1.4.1          tidyselect_0.2.5       xfun_0.4