RnaBindingProtein: RnaBindingProtein

In paul-shannon/rnaBindingProteins: RnaBindingProtein

Description

assess RNA-binding protein binding sites, their structure and motif matches

Public fields

rbp

the gene symbol name of the protein

Active bindings

rbp

the gene symbol name of the protein

Methods

Public methods

• RnaBindingProtein$new()

• RnaBindingProtein$getEncodeCatalog()

• RnaBindingProtein$getBindingTable()

• RnaBindingProtein$getAnnotationTypes()

• RnaBindingProtein$start.igv()

• RnaBindingProtein$getGenicRegions()

• RnaBindingProtein$getAllGenicAnnotations()

• RnaBindingProtein$getBindingSites()

• RnaBindingProtein$getGeneRegion()

• RnaBindingProtein$getBindingSites.inGenicRegions()

• RnaBindingProtein$runMeme()

• RnaBindingProtein$clone()

---

Method new()

Creates a new instance of this [R6][R6::R6Class] class.

Usage

RnaBindingProtein$new(rbp, targetGene, cellType, motifs.meme.file = NA)

Arguments

targetGene

character, gene symbol presumably having associated rbp binding sites

cellType

character, currently "K562" or "HepG2"

motifs.meme.file

character, full path to an optional motifs file, calculated separately, describing motifs for the rbp

rpb

character, gene symbol identifier for the rbp

---

Method getEncodeCatalog()

Usage

RnaBindingProtein$getEncodeCatalog()

Returns

the table of RBPs/cellTypes for which we have bigBed files from ENCODE

---

Method getBindingTable()

Usage

RnaBindingProtein$getBindingTable()

Returns

the slightly processed and filtered data.frame version of the ENCODE bigbed

---

Method getAnnotationTypes()

the bioc annotatr class offers a large set of genic annotations, ultimately obtained from UCSC via TxDb.Hsapiens.UCSC.hg38.knownGene

Usage

RnaBindingProtein$getAnnotationTypes()

Returns

genic annotation types for hg38

---

Method start.igv()

start, and retain a reference to, an igvR for the current genome and targetGene

Usage

RnaBindingProtein$start.igv()

Returns

igv reference

---

Method getGenicRegions()

extract all genic regions, mulitiple types, no longer just 3' and 5' UTRs and CDS) for the targetGene

Usage

RnaBindingProtein$getGenicRegions()

Returns

data.frame

---

Method getAllGenicAnnotations()

access to the full whole genome annotations table

Usage

RnaBindingProtein$getAllGenicAnnotations()

Returns

data.frame

---

Method getBindingSites()

retrieve the rbp bindings sites within the specified region

Usage

RnaBindingProtein$getBindingSites(roi)

Arguments

roi

list with chrom, start, end fields

Returns

data.frame

---

Method getGeneRegion()

retrieve the chrom, start and end of the targetGene, if !na

Usage

RnaBindingProtein$getGeneRegion()

Returns

list with chrom, start end, geneSymbol fields

---

Method getBindingSites.inGenicRegions()

retrieve the rbp bindings which intersect with annotated genic regions of interest, currently UTRs and CDSfor the targetGene

Usage

RnaBindingProtein$getBindingSites.inGenicRegions(intersectionType = "within")

Arguments

intersectionType

character, one of "any" or "within"

Returns

data.frame

---

Method runMeme()

create fasta file from filtered rbp binding sites, run meme

Usage

RnaBindingProtein$runMeme(tag.name, bl.sitesFiltered)

Arguments

tagName

character something memorable and explanatory

top.quartiles.to.include

numeric, 1 or more

Returns

character string, the path to the meme html output

---

Method clone()

The objects of this class are cloneable with this method.

Usage

RnaBindingProtein$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

  rbp <- RnaBindingProtein("DDX3X", "path/to/ENCFF565FNW.bigBed", "K562", "path/to/ddx3x.meme")

paul-shannon/rnaBindingProteins documentation built on Feb. 14, 2022, 1:56 a.m.