createRetainedIntronSplicingMap • RNAPeaks

Overview

createRetainedIntronSplicingMap() quantifies RBP binding frequency around the two junctions of retained-intron (RI) events: the upstream exon/intron boundary and the downstream intron/exon boundary. It accepts the same SE.MATS column format and the same parameters as createSplicingMap().

library(RNAPeaks)

Basic usage

createRetainedIntronSplicingMap(
    bed_file = sample_bed,
    RIMATS   = sample_se.mats
)

Event classification

Events are classified using the same thresholds as createSplicingMap():

Retained — IncLevelDifference < -0.1
Excluded — IncLevelDifference > 0.1
Control — non-significant, stable inclusion

createRetainedIntronSplicingMap(
    bed_file                     = sample_bed,
    RIMATS                       = sample_se.mats,
    retained_IncLevelDifference  = -0.1,
    exclusion_IncLevelDifference = 0.1,
    p_valueRetainedAndExclusion  = 0.05,
    p_valueControls              = 0.95,
    Min_Count                    = 50
)

Bootstrap control and significance

The same bootstrap z-score approach is used as in createSplicingMap(). See the createSplicingMap article for full details.

createRetainedIntronSplicingMap(
    bed_file           = sample_bed,
    RIMATS             = sample_se.mats,
    control_iterations = 30,
    use_fdr            = TRUE,
    fdr_threshold      = 0.05,
    show_significance  = TRUE
)

Returning data

freq_df <- createRetainedIntronSplicingMap(
    bed_file    = sample_bed,
    RIMATS      = sample_se.mats,
    return_data = TRUE
)
head(freq_df)