mepHuman: Main setup for Mutations Exon Plot

Description

Creates all main variables using the human genome from databases and objects, passes variables and input data to interface function

Usage

mepHuman(m.data, gui = FALSE)

Arguments

m.data

Mutations data.frame or GRanges object which contains at minimum Chromosome, Start Position, End Position, and Strand data. It may also contain a column which uniquely identifies each mutation for legend plotting.

gui

Determines whether the GUI is used.

Value

A mutExonPlot using the hg19 platform

Details

The mepHuman function creates the following objects which are passed to mepGui or mepTxtInt:

tx.db UCSC hg19 known Gene database from TxDb.Hsapiens.UCSC.hg19.knownGene

genesymbol GRanges object describing human genes from genesymbol

seqs.hg19 seqlengths of hg19 object

pfam.gr, pfam.desc, pfam.ids objects containing PFAM domain information

int.opt, disp.opt character vectors which describe the plotting input choices

Examples

Run this code

if (interactive()) {
  # Create a missense mutations dataset in TP53
  set.seed(1)
  locations = sample(7571720:7590863, size = 25)
  mut.df <- data.frame(chrom = "chr17", 
                      start = locations, 
                      end = locations, 
                      strand = "-", 
                      fill = 1:25)
  
  library(gWidgetsRGtk2)
  library(RGtk2)
  
  # GUI example
  mepHuman(m.data = mut.df, gui = TRUE)
}

if (interactive()) {
  # Text interface example
  mepHuman(m.data = mut.df)
}