R API Reference

R API Reference#

Arrow IPC readers#

The following functions return binary blobs of data in Arrow IPC format (formerly known as Feather). To read the output into a tibble or Arrow table and interface with dplyr use the R arrow package. For example:

library(oxbow)
library(arrow)

ipc <- oxbow::read_bam("example.bam", region="chr1:1-10000")
df <- arrow::read_feather(ipc)

Sequence formats#

read_fastq#

Return Arrow IPC format from a FASTQ file.

oxbow::read_fastq(path, fields = NULL)

read_fasta#

Return Arrow IPC format from a FASTA file.

oxbow::read_fasta(path, regions = NULL, index = NULL, gzi = NULL, fields = NULL)

Alignment formats#

read_sam#

Return Arrow IPC format from a SAM file.

oxbow::read_sam(path, region = NULL, index = NULL, fields = NULL, scan_rows = NULL)

read_bam#

Return Arrow IPC format from a BAM file.

oxbow::read_bam(path, region = NULL, index = NULL, fields = NULL, scan_rows = NULL)

Variant call formats#

read_vcf#

Return Arrow IPC format from a VCF file.

oxbow::read_vcf(path, region = NULL, index = NULL, fields = NULL, info_field = NULL, genotype_fields = NULL, genotype_by = "sample")

read_bcf#

Return Arrow IPC format from a BCF file.

oxbow::read_bcf(path, region = NULL, index = NULL, fields = NULL, info_fields = NULL, genotype_fields = NULL, genotype_by = "sample")

Interval feature formats#

read_gtf#

Return Arrow IPC format from a GTF file.

oxbow::read_gtf(path, region = NULL, index = NULL, fields = NULL, scan_rows = NULL)

read_gff#

Return Arrow IPC format from a GFF file.

oxbow::read_gff(path, region = NULL, index = NULL, fields = NULL, scan_rows = NULL)

read_bed#

Return Arrow IPC format from a BED file.

oxbow::read_bed(path, bed_schema, region = NULL, index = NULL, fields = NULL)

UCSC BBI formats#

read_bigwig#

Return Arrow IPC format from a BigWig file.

oxbow::read_bigwig(path, region = NULL, fields = NULL)

read_bigbed#

Return Arrow IPC format from a BigBed file.

oxbow::read_bigbed(path, bed_schema = "bed3+", region = NULL, fields = NULL)
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