Outputs GRangesList object from reading a GTF file
readFromGTF(file, keep.extra.columns = NULL)
| file | a .gtf file |
|---|---|
| keep.extra.columns | a vector with names of columns to keep from the the attributes in the gtf file. For ensembl, this could be keep.extra.columns=c('gene_name','gene_biotype', 'transcript_biotype', 'transcript_name') |
grlist a GRangesList object, with two columns
specifying prefix for new gene Ids (genePrefix.number), defaults to empty
indicating whether filter to remove read classes which are a subset of known transcripts(), defaults to TRUE
gtf.file <- system.file("extdata", "Homo_sapiens.GRCh38.91_chr9_1_1000000.gtf", package = "bambu" ) readFromGTF(gtf.file) #> GRangesList object of length 105: #> $ENST00000190165 #> GRanges object with 2 ranges and 1 metadata column: #> seqnames ranges strand | exon_rank #> <Rle> <IRanges> <Rle> | <character> #> [1] 9 976964-977455 + | 1 #> [2] 9 990041-991731 + | 2 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengths #> #> $ENST00000305248 #> GRanges object with 2 ranges and 1 metadata column: #> seqnames ranges strand | exon_rank #> <Rle> <IRanges> <Rle> | <character> #> [1] 9 34965-35264 - | 2 #> [2] 9 35504-35871 - | 1 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengths #> #> $ENST00000314367 #> GRanges object with 16 ranges and 1 metadata column: #> seqnames ranges strand | exon_rank #> <Rle> <IRanges> <Rle> | <character> #> [1] 9 121060-121573 - | 16 #> [2] 9 121961-122090 - | 15 #> [3] 9 123217-123282 - | 14 #> [4] 9 123386-123454 - | 13 #> [5] 9 134979-135030 - | 12 #> ... ... ... ... . ... #> [12] 9 172081-172172 - | 5 #> [13] 9 173270-173366 - | 4 #> [14] 9 175698-175784 - | 3 #> [15] 9 177723-177820 - | 2 #> [16] 9 178816-179047 - | 1 #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengths #> #> ... #> <102 more elements>