View-Reference-methods: View SpliceWiz Reference in read-able data frames

In alexchwong/SpliceWiz: interactive analysis and visualization of alternative splicing in R

View SpliceWiz Reference in read-able data frames

Description

These functions allow users to construct tables containing SpliceWiz's reference of alternate splicing events, intron retention events, and other relevant data

Usage

viewASE(reference_path)

viewIR(reference_path, directional = TRUE)

viewIntrons(reference_path)

viewIR_NMD(reference_path)

viewExons(reference_path)

viewGenes(reference_path)

viewGO(reference_path)

viewProteins(reference_path)

viewTranscripts(reference_path)

Arguments

reference_path	The directory containing the SpliceWiz reference
directional	(default TRUE) Whether to view IR events for stranded RNAseq TRUE or unstranded protocol FALSE

Value

A data frame containing the relevant info. See details

Functions

• viewASE(): Outputs summary of alternative splicing events constructed by SpliceWiz

• viewIR(): Outputs summary of assessed IRFinde-like IR events, constructed by SpliceWiz

• viewIntrons(): Outputs summary of all introns from the annotation, constructed by SpliceWiz

• viewIR_NMD(): Outputs information for every intron - whether retention of the intron will convert the transcript to an NMD substrate

• viewExons(): Outputs information for every exon from the annotation.

• viewGenes(): Outputs information for every gene from the annotation.

• viewGO(): Outputs information for every gene from the annotation.

• viewProteins(): Outputs information for every protein-coding exon from the annotation.

• viewTranscripts(): Outputs information for every transcript from the annotation.

See Also

Build-Reference-methods

Examples

ref_path <- file.path(tempdir(), "Reference_withGO")
buildRef(
    reference_path = ref_path,
    fasta = chrZ_genome(),
    gtf = chrZ_gtf(),
    ontologySpecies = "Homo sapiens"
)

df <- viewASE(ref_path)

df <- viewIR(ref_path, directional = TRUE)

df <- viewIntrons(ref_path)

df <- viewIR_NMD(ref_path)

df <- viewExons(ref_path)

df <- viewGenes(ref_path)

df <- viewProteins(ref_path)

df <- viewTranscripts(ref_path)

df <- viewGO(ref_path)

alexchwong/SpliceWiz documentation built on Oct. 15, 2024, 10:12 a.m.