EzRef-class: The S4 class representing a collection of information about...

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

The S4 class representing a collection of information about the reference build

Description

Objects of this class are a collection of references derived from a list of parameters.

Usage

## S4 method for signature 'EzRef'
initialize(.Object, param = list())

## S4 method for signature 'EzRef,ANY,ANY,ANY'
x[i]

## S4 replacement method for signature 'EzRef,ANY,ANY,ANY'
x[i] <- value

## S4 method for signature 'EzRef'
getOrganism(.Object)

## S4 method for signature 'EzRef'
buildRefDir(.Object, genomeFile, genesFile, genomesRoot = ".")

## S4 method for signature 'EzRef'
buildIgvGenome(.Object)

Methods (by generic)

• initialize: Initializes the slots of EzRef. It will also try to specify some fields and if necessary get full file paths.

• [: Access of slots by name with square brackets [ ]

• [<-: Assignment to slots by name with square brackets [ ]

• getOrganism: Gets the organism name from the reference build.

• buildRefDir: Builds the reference directory and copies the annotation and fasta file into the right folders.

• buildIgvGenome: Builds the IGV genome.

Slots

refBuild

a character specifying the file path to the reference build.

refBuildName

a character specifying the name of the reference build.

refBuildDir

a character specifying the directory of the reference build.

refIndex

a character specifying the location of the index that is used in the alignment.

refFeatureFile

a character specifying the file path to the annotation feature file (.gtf).

refAnnotationFile

a character specifying the file path to the annotation file (.txt). Subsetting species are automatically removed

refFastaFile

a character specifying the file path to the fasta file.

refChromSizesFile

a character specifying the file path to the file containing the chromosome sizes.

refAnnotationVersion

a character specifying the annotation version.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

cleanGenomeFiles

Examples

refBuild = "Saccharomyces_cerevisiae/Ensembl/EF4/Annotation/Version-2013-03-18"
genomesRoot = "./refExample"
param = ezParam(list(refBuild=refBuild, genomesRoot=genomesRoot))
gtf = system.file("extdata/genes.gtf", package="ezRun", mustWork = TRUE)
fp = system.file("extdata/genome.fa", package="ezRun", mustWork = TRUE)
buildRefDir(param$ezRef, fp, gtf)
buildIgvGenome(param$ezRef)
seqAnno = writeAnnotationFromGtf(param=param)

uzh/ezRun documentation built on April 24, 2024, 4:01 p.m.