I have an error when performing a DEXseq count for exon usuage from RNA-seq data.
DEXSeqDataSetFromSE( SE, design= ~ sample + exon + condition:exon )
I receive the error: Error in DEXSeqDataSetFromSE(SE, design = ~sample + exon + condition:exon) :
make sure your SummarizedExperiment object contain the columns gene_id, tx_name and exonic_part
Any help would be appreciated.
This is the full code
library(DEXSeq)
library(GenomicRanges)
library(GenomicFeatures)
library(GenomicAlignments)
library(biomaRt)
hse = makeTxDbFromBiomart( biomart="ensembl", dataset="mmusculus_gene_ensembl", host="ensembl.org")
library(txdb.mmusculus.ucsc.mm10.knowngene)
exonicParts = exonicParts( hse, linked.to.single.gene.only = TRUE )
list.files(pattern=".bam$")
fls = list.files(pattern="bam$", full=TRUE )
bamlst = BamFileList( fls, index=character(), yieldSize=100000, obeyQname=TRUE )
SE = summarizeOverlaps( exonicParts, bamlst, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, inter.feature=FALSE, fragments=TRUE )
DEXSeqDataSetFromSE( SE, design= ~ sample + exon + condition:exon )
Error in DEXSeqDataSetFromSE(SE, design = ~sample + exon + condition:exon) :
make sure your SummarizedExperiment object contain the columns gene_id, tx_name and exonic_part
**Session Info:**
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.38.0 GenomicAlignments_1.18.1 Rsamtools_1.34.1
[4] Biostrings_2.50.2 XVector_0.22.0 GenomicFeatures_1.34.8
[7] DEXSeq_1.28.3 RColorBrewer_1.1-2 AnnotationDbi_1.44.0
[10] DESeq2_1.22.2 SummarizedExperiment_1.12.0 DelayedArray_0.8.0
[13] matrixStats_0.54.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2
[16] IRanges_2.16.0 S4Vectors_0.20.1 Biobase_2.42.0
[19] BiocGenerics_0.28.0 BiocParallel_1.16.6
loaded via a namespace (and not attached):
[1] httr_1.4.0 bit64_0.9-7 splines_3.5.2 assertthat_0.2.1
[5] Formula_1.2-3 statmod_1.4.30 BiocManager_1.30.4 latticeExtra_0.6-28
[9] blob_1.1.1 GenomeInfoDbData_1.2.0 progress_1.2.1 pillar_1.4.0
[13] RSQLite_2.1.1 backports_1.1.4 lattice_0.20-38 digest_0.6.18
[17] checkmate_1.9.3 colorspace_1.4-1 htmltools_0.3.6 Matrix_1.2-17
[21] plyr_1.8.4 XML_3.98-1.19 pkgconfig_2.0.2 genefilter_1.64.0
[25] zlibbioc_1.28.0 xtable_1.8-4 snow_0.4-3 scales_1.0.0
[29] htmlTable_1.13.1 tibble_2.1.1 annotate_1.60.1 ggplot2_3.1.1
[33] nnet_7.3-12 lazyeval_0.2.2 survival_2.44-1.1 magrittr_1.5
[37] crayon_1.3.4 memoise_1.1.0 hwriter_1.3.2 foreign_0.8-71
[41] prettyunits_1.0.2 tools_3.5.2 data.table_1.12.2 hms_0.4.2
[45] stringr_1.4.0 munsell_0.5.0 locfit_1.5-9.1 cluster_2.0.9
[49] compiler_3.5.2 rlang_0.3.4 grid_3.5.2 RCurl_1.95-4.12
[53] rstudioapi_0.10 htmlwidgets_1.3 bitops_1.0-6 base64enc_0.1-3
[57] gtable_0.3.0 curl_3.3 DBI_1.0.0 R6_2.4.0
[61] gridExtra_2.3 rtracklayer_1.42.2 knitr_1.22 bit_1.1-14
[65] Hmisc_4.2-0 stringi_1.4.3 Rcpp_1.0.1 geneplotter_1.60.0
[69] rpart_4.1-15 acepack_1.4.1 xfun_0.7
Did you do that? Check the DEXseq manual on
#Requirements on GTF files
.