Package index

All functions

calc_a3ss_a5ss()

Function to calcualte 5' and 3' alternative splice sites given a GRanges object

calc_mutually_exclusive()

Calculate mutually exclusive exons from a GRanges object

calc_retained_introns()

Function to calculate retained introns given a GRanges object

calc_skipped_exons()

Calculate skipped exons from a GRanges object

candidates_by_non_overlap_directed()

Filter candidates that do not overlap any pos_exons, and are internal Then get the left and right exons for each candidate Return a named list with three GRanges objects: candidates, left_exons, right_exons

create_mock_data()

Create mock GRanges data for splicing event testing

find_candidates()

Find candidates skipped exons

generate_a3ss()

Generate alternative 3' splice site events in a GRanges object

generate_a5ss()

Generate alternative 5' splice site events in a GRanges object

generate_retained_introns()

Generate retained intron events in a GRanges object

generate_skipped_exons()

Generate skipped exon events in a GRanges object making all >0 coefs transcripts have a the same exon eventfor the same gene

generate_skipped_exons_restricted()

Generate skipped exon events in a GRanges object making all >0 coefs transcripts have a the same exon eventfor the same gene

mx_mock_data()

Create a sample GRanges with one negative coef transcript and one positive coef transcripts This dataset is designed to include a mutually exclusive exons between exon_rank 3 of tx_id 1 and exon_rank 3 of tx_id 2. There is also a skipped exon event at exon_rank 5 of tx_id 1.

no_event_mock_data()

Create a sample GRanges with one negative coef transcript and one positive coef transcripts This dataset is designed to include no splicing events

preprocess_input()

Preprocess input GRanges object for splicing event calculation

se_mock_data()

Create a sample GRanges with one negative coef transcript and two positive coef transcripts This dataset is designed to include a skipped exon event at exon_rank 3 and 5 of tx_id 1 happening between both tx_id 2 and tx_id 3