A.9 Reading Genomic Files
We provide convenience functions via rtracklayer and GenomicAlignments for reading/writing the following data formats to/from Ranges objects.
| plyranges functions | File Format |
|---|---|
read_bam() |
BAM |
read_bed()/write_bed() |
BED |
read_bed_graph()/ write_bed_graph() |
BEDGraph |
read_narrowpeaks()/write_narrowpeaks() |
narrowPeaks |
read_gff() / write_gff() |
GFF(1-3)/ GTF |
read_bigwig() / write_bigwig() |
BigWig |
read_wig() /write_wig() |
Wig |