getDetails: Gathers details from biomaRt

In FIRMAGene: FIRMAGene - differential splicing for Affymetrix Gene 1.0 ST

Description

Given a ProbeLevelModel object and information regarding the probes (start and stop locations), this function retrieves public information from Biomart

Usage

getDetails(plm, probesets, id = "7952953", mart = NULL, verticalBars=FALSE, geneSymbolId="external_gene_id", transcriptClusterId="Transcript.Cluster.ID", colours = "blue", lwd = 1, o = NULL, verbose = FALSE)

Arguments

plm	a ProbeLevelModel object
probesets	a data.frame object giving the coordinates, must have the following columns: start, stop, seqname (chromosome)
id	identifier to gather annotation details for
mart	a mart returned from useMart
verticalBars	logical, whether to draw vertical bars between probes/probesets
geneSymbolId	the Ensembl/biomaRt column to use as
transcriptClusterId	the column of the probesets dataframe to match the id on
colours	scalar or vector (of the same length as the number of samples) to use for line plot colours
lwd	scalar or vector (of the same length as the number of samples) to use for line plot widths
o	order to reorder plotting of lines
verbose	logical, whether to print out progress comments.

Details

This function gathers the raw data and residuals as 'ExonArray' objects (see GenomeGraphs) and creates a 'GeneRegion' object for the gene selected. A list is returned which can be plotted with 'gdPlot'

Value

a 'list' object that can be plotted with 'gdPlot' (from GenomeGraphs)

Author(s)

Mark Robinson

Examples

## not run

FIRMAGene documentation built on May 2, 2019, 5:55 p.m.