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Update TxDb creation method in rnaseq_gene_level.Rmd for newer Bioconductor versions #111

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Update TxDb creation method in rnaseq_gene_level.Rmd for newer Bioconductor versions #111

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7 changes: 7 additions & 0 deletions rnaseq/rnaseq_gene_level.Rmd
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Expand Up @@ -37,9 +37,16 @@ Next we create an *Rsamtools* variable which wraps our BAM files, and create a t
library(Rsamtools)
bam.list <- BamFileList(bam.files)
library(GenomicFeatures)

# for Bioc 3.0 use the commented out line
# txdb <- makeTranscriptDbFromGFF(gtf.file, format="gtf")
txdb <- makeTxDbFromGFF(gtf.file, format="gtf")

# Since the Bioc V-3.19, `makeTxDbFromGFF()` is defuncted in 'GenomicFeatures' package.The function has now moved to the 'txdbmaker' package;
#therefore, for Bioc V-3.19 and higher, use `txdbmaker::makeTxDbFromGFF()` function instead.
#library(txdbmaker)
#txdb <- makeTxDbFromGFF(gtf.file, format="gtf")

exons.by.gene <- exonsBy(txdb, by="gene")
```

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