Removes isoform annotations that could produce ambigious reads, such as isoforms that only differ by the 5' / 3' end. This could be useful for plotting average coverage plots.
Arguments
- annotation
path to the GTF annotation file, or the parsed GenomicRanges object with a valid
transcript_idcolumn, and each Range representing a transcript.- keep
string, one of 'tss_differ' (only keep isoforms that all differ by the transcription start site position), 'tes_differ' (only keep those that differ by the transcription end site position), 'both' (only keep those that differ by both the start and end site), or 'single_transcripts' (only keep genes that contains a sinlge transcript).
Examples
filtered_annotation <- filter_annotation(
system.file("extdata", "rps24.gtf.gz", package = 'FLAMES'), keep = 'tes_differ')
filtered_annotation
#> GRanges object with 6 ranges and 18 metadata columns:
#> seqnames ranges strand | source type score phase
#> <Rle> <IRanges> <Rle> | <factor> <factor> <numeric> <integer>
#> [1] chr14 19-5159 + | HAVANA transcript NA <NA>
#> [2] chr14 32-3389 + | HAVANA transcript NA <NA>
#> [3] chr14 68-5124 + | HAVANA transcript NA <NA>
#> [4] chr14 86-1118 + | HAVANA transcript NA <NA>
#> [5] chr14 160-2761 + | HAVANA transcript NA <NA>
#> [6] chr14 450-1290 + | HAVANA transcript NA <NA>
#> gene_id transcript_id gene_type gene_name
#> <character> <character> <character> <character>
#> [1] ENSMUSG00000025290.17 ENSMUST00000225994.1 protein_coding Rps24
#> [2] ENSMUSG00000025290.17 ENSMUST00000225117.1 protein_coding Rps24
#> [3] ENSMUSG00000025290.17 ENSMUST00000224568.1 protein_coding Rps24
#> [4] ENSMUSG00000025290.17 ENSMUST00000224549.1 protein_coding Rps24
#> [5] ENSMUSG00000025290.17 ENSMUST00000224569.1 protein_coding Rps24
#> [6] ENSMUSG00000025290.17 ENSMUST00000224699.1 protein_coding Rps24
#> transcript_type transcript_name level protein_id
#> <character> <character> <character> <character>
#> [1] retained_intron Rps24-212 2 <NA>
#> [2] processed_transcript Rps24-211 2 <NA>
#> [3] protein_coding Rps24-207 2 ENSMUSP00000153637.1
#> [4] processed_transcript Rps24-206 2 <NA>
#> [5] processed_transcript Rps24-208 2 <NA>
#> [6] processed_transcript Rps24-209 2 <NA>
#> transcript_support_level mgi_id tag ccdsid
#> <character> <character> <character> <character>
#> [1] <NA> MGI:98147 <NA> <NA>
#> [2] <NA> MGI:98147 <NA> <NA>
#> [3] <NA> MGI:98147 basic <NA>
#> [4] <NA> MGI:98147 mRNA_end_NF <NA>
#> [5] <NA> MGI:98147 <NA> <NA>
#> [6] <NA> MGI:98147 mRNA_end_NF <NA>
#> havana_gene havana_transcript
#> <character> <character>
#> [1] OTTMUSG00000068639.1 OTTMUST00000165910.1
#> [2] OTTMUSG00000068639.1 OTTMUST00000165914.1
#> [3] OTTMUSG00000068639.1 OTTMUST00000165915.1
#> [4] OTTMUSG00000068639.1 OTTMUST00000165916.1
#> [5] OTTMUSG00000068639.1 OTTMUST00000165917.1
#> [6] OTTMUSG00000068639.1 OTTMUST00000165918.1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths