junction_inclusion_ratio: Relative measure of splice variant usage similar to PSI that...

In langmead-lab/snapr: R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

Relative measure of splice variant usage similar to PSI that allows for 2 arbitrarily defined groups of junctions (not limited to cassette exons).

Description

Calculates a coverage summary statistic per sample of the normalized coverage difference between two sets of separate junctions defined by at least two basic queries and organized into two groups.

Usage

junction_inclusion_ratio(group1, group2, group_names = NULL)

Arguments

group1, group2	Each group is a list of 1 or more QueryBuilder objects
group_names	Optional vector of strings representing the group names

Details

The summary statistic is as follows: If the coverage of the first group is "A" and the second is "B":

JIR(A,B)=(A - B) / (A+B+1)

This is calculated for every sample that occurs in one or the other (or both) groups results.

Value

A DataFrame of samples, with their JIR score and metadata, which had > 0 coverage in at least one resulting row in at least one of the groups

Examples

sb1 <- QueryBuilder(compilation = "srav2", regions = "chr2:29446395-30142858")
sb1 <- set_coordinate_modifier(sb1, Coordinates$Within)
sb1 <- set_row_filters(sb1, strand == "-")

sb2 <- QueryBuilder(compilation = "srav2", regions = "chr2:29416789-29446394")
sb2 <- set_coordinate_modifier(sb2, Coordinates$Within)
sb2 <- set_row_filters(sb2, strand == "-")

junction_inclusion_ratio(list(sb1), list(sb2))

langmead-lab/snapr documentation built on May 4, 2022, 7:41 p.m.