writeAnnotationFromGtf: Feature annotation file operations

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

Feature annotation file operations

Description

Gets the sequence annotation from annotation (gtf or gff) and sequence (fasta) information. Sequence annotation files are on the isoform level. If the analysis is to be done at the gene level, the annotation for the isoforms is aggregated.

Usage

  writeAnnotationFromGtf(param, featureFile = param$ezRef@refFeatureFile,
                         featAnnoFile = param$ezRef@refAnnotationFile)
  aggregateGoAnnotation(seqAnno, genes,
                        goColumns = c("GO BP", "GO CC", "GO MF"))

Arguments

param	the parameters to load the annotation and sequence files from and possibly write to.
ids	a character vector containing the gene ID's to return.
dataFeatureType	either "isoform" or "gene".

Value

Returns a data.frame containing information about the genes in an easily readable way.

Functions

• writeAnnotationFromGtf: Gets the annotation from a .gtf file and transforms it into a tab-separated tabular .txt file.

• aggregateGoAnnotation: Aggregates the Go annotation.

Author(s)

Rehrauer, Hubert

Schmid, Peter

Examples

param = ezParam()
param$ezRef["refFeatureFile"] = system.file("extdata/genes.gtf", package="ezRun", mustWork=TRUE)
param$ezRef["refFastaFile"] = system.file("extdata/genome.fa", package="ezRun", mustWork=TRUE)
annoFile = system.file("extdata/genes_annotation.txt", package="ezRun", mustWork=TRUE)
param$ezRef["refAnnotationFile"] = annoFile
seqAnno = writeAnnotationFromGtf(param)
seqAnno2 = ezFeatureAnnotation(param, rownames(seqAnno), dataFeatureType="gene")

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