rna_majiq.SJIntronsBins

class rna_majiq.SJIntronsBins(sj_intronsbins, strandness, original_path, original_version, original_time, prefix=None, gene_introns_checksum=None, exons_checksum=None, **additional_metadata)

Per-bin read coverage over introns

Parameters:

sj_intronsbins (_SJIntronsBins) – Underlying object binding the internal C++ API
strandness (ExperimentStrandness) – strandness that was used for the experiment
original_path (str) – Original path to BAM file from which coverage was derived
original_version, original_time (str) – Version of MAJIQ and time BAM file was processed
gene_introns_checksum, exons_checksum (Optional[int]) – Checksum of gene introns, exons used to define regions for coverage

Notes

Intron coverage is dependent on the gene introns and exons used to define regions on which to assess coverage.

See also

SJExperiment.from_bam, SJIntronsBins.from_bam, SJIntronsBins.from_zarr

__init__(sj_intronsbins, strandness, original_path, original_version, original_time, prefix=None, gene_introns_checksum=None, exons_checksum=None, **additional_metadata)

Methods

`__init__`(sj_intronsbins, strandness, ...[, ...])
`from_arrays`(regions, bin_reads, bin_idx, ...)	Create `SJIntronsBins` from `SJIntrons`, arrays, metadata
`from_bam`(path, total_bins, exons, gene_introns)	Load SJIntronsBins from BAM file
`from_regions`(introns, total_bins[, ...])	Empty SJIntronsBins matched to input introns
`from_zarr`(store)	Load SJIntronsBins from zarr format
`numbins`([region_idx, minreads])	Number of bins for regions with at least specified number of reads
`numreads`([region_idx, numstacks])	Calculate total number of reads at specified regions with stacks
`numstacks`([region_idx, pvalue_threshold])	Calculate number of stacks at specified regions/pvalues
`rename_prefix`(new_prefix)	Create updated self where self.prefix is set to new_prefix
`to_zarr`(store[, consolidated, ...])	Serialize to zarr format

Attributes

`IDX_NAME`
`bin_idx`	index of each bin on each region
`bin_reads`	number of reads for each region/bin
`bin_reads_2d`	2D array representation of reads per region/bin
`df`	View of read counts per bin (combined with underlying regions)
`exons_checksum`	checksum of introns used in constructing `SJIntronsBins`
`gene_introns_checksum`	checksum of introns used in constructing `SJIntronsBins`
`original_path`
`original_time`
`original_version`
`prefix`	Experiment name associated with these bin reads.
`regions`
`sib_idx`
`sib_idx_end`
`sib_idx_start`
`strandness`
`total_bins`	total possible number of bins (defined by positions for junctions)