bed_overlap: Applied to check the distance between each STR site and...

In huanglu2018/tSTR: functions used in gtex2str project

Description

Applied to check the distance between each STR site and closest exon boundaries, if too close, it might be disturbed by alternative splicing(AS), alternative polyadenylation(APA), or alternative promoter usage(APU) events

Usage

bed_overlap(query_bed, ref_bed)

Arguments

query_bed	bed3 or more cols to check their overlap with references
ref_bed	bed files as reference, when extracting from gtf, careful about differences between 0-index and 1-index

Value

combined df with two more columns, "inside_distance_to_ref_boundary" and "outside_distance_to_ref_boundary"; inside_distance_to_ref_boundary=0 means not inside or just at the boundary, outside_distance_to_ref_boundary=0 means not outside or just at the boundary

huanglu2018/tSTR documentation built on Feb. 25, 2022, 5:39 a.m.