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createRetainedIntronSequenceMap

Source: vignettes/ri-sequence-map.Rmd
ri-sequence-map.Rmd

Overview

createRetainedIntronSequenceMap() measures per-position sequence motif frequency at retained-intron junctions using the same two-bin window as createRetainedIntronSplicingMap(). It accepts the same parameters as createSequenceMap() with RIMATS in place of SEMATS.

Basic usage 

library(BSgenome.Hsapiens.UCSC.hg38)

createRetainedIntronSequenceMap(
    RIMATS   = sample_se.mats,
    sequence = "YCAY"
)

Multiple motifs 

plots <- createRetainedIntronSequenceMap(
    RIMATS   = sample_se.mats,
    sequence = c("YCAY", "YGCY")
)
plots[["YCAY"]]

Using a custom genome 

library(BSgenome.Mmusculus.UCSC.mm10)

createRetainedIntronSequenceMap(
    RIMATS   = sample_se.mats,
    sequence = "YCAY",
    genome   = BSgenome.Mmusculus.UCSC.mm10
)

IUPAC codes and returning data

The full IUPAC code table and return_data behavior are identical to createSequenceMap(). See the createSequenceMap article for details.