ezLoadFeatures: Loads annotation features from a file

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

Loads annotation features from a file

Description

Loads annotation features from a file and returns them as a data.frame.

Usage

  ezLoadFeatures(param = NULL, featureFile = param$ezRef["refFeatureFile"], 
                 types = NULL)
  addPromotersToGff(gff, promWidth)

Arguments

param	contains the feature file and possibly a logical called addPromoters, which will add promoters if set to true.
featureFile	the file to load the features from.
types	a character vector containing the types.

Value

Returns a data.frame of parsed features.

Functions

• ezGffAttributeField: Gets the attribute from the specified field.

• addPromotersToGff: Adds promoters to the gff list if addPromoters is specified.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

ezReadGff

Examples

  ## Not run: 
    param = ezParam()
    gtfFile = system.file("extdata/genes.gtf", package="ezRun", mustWork=TRUE)
    gtf = ezLoadFeatures(param, gtfFile)
    attrField = ezGffAttributeField(gtf$attributes, field="transcript_id", 
                                    attrsep="; *", valuesep=" ")
    addPromotersToGff(gtf, promWidth=300L)
  
## End(Not run)

uzh/ezRun documentation built on Sept. 16, 2024, 11:21 p.m.