loadGafModels: Load a GAF models file into a per exon data frame.

In jefferys/FusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description

Load a GAF models file into a per exon data frame.

Usage

loadGafModels(file)

Arguments

file	The file of models extracted from the GAF.

Value

Returns a per-exon data frame of the models extracted from the GAF. Most models (e.g. genes or transcripts) are composed of multiple exons with each features-exon in separate row. For convenience, the table replicates a lot of information that is the same for every exon in a model as a string, i.e columns gene, chr, strand, gstart, and gend).

The data frame contains the following columns

gene	Feature name - gene name, transcript id, etc.
chr	Chromosome, as chr#, chr##, chrX, chrY, chrM, or chrM_rCRS or possibly a contig name, like 'GL000228.1'.
strand	Strand, as *, +, or -
gstart	Genomic coordinate of first base of feature
gend	Genomic coordinate of last base of feature
exon	Exon number within feature
start	Genomic coordinate of first base of exon
end	Genomic coordinate of last base of exon
length	length of the exon in bases

Todo

• change column named "gene" to "name"

• add column "gafId"

• consider an alias column with | separated names

• change gstart and gend to mstart and mend

Errors

These errors are fatal and will terminate processing.

Can't find the specified GAF extract file: "file"

The specified GAF doesn't seem to exist on the file system. Probably have the name wrong or are using a relative name from the wrong directory, but could also be that permissions are hiding it.

Examples

## Not run: 

extractGeneModels( 'TCGA.hg19.June2011.gaf' )
gafGeneModelsFile <- 'TCGA.hg19.June2011.gaf.geneModels'
geneExonsDF <- loadGafModels( gafTranscriptModelsFile )

extractTranscriptModels( 'TCGA.hg19.June2011.gaf' )
gafTranscriptModelsFile <- 'TCGA.hg19.June2011.gaf.transcriptModels'
transcriptExonsDF <- loadGafModels( gafTranscriptModelsFile )

## End(Not run)

jefferys/FusionExpressionPlot documentation built on May 19, 2019, 3:59 a.m.