GenoView (version 1.6.0)

mep-Interfaces: Interfaces for MutExonPlot

Description

Package interfaces which create, display, and save Mutations-Over-Exons plots in succession.

Usage

mepGUI(m.data, tx.db, gene.loc, seq.lens, pfam.gr = NULL, pfam.desc = NULL,
pfam.ids = NULL, ...)
mepTxtInt(m.data, tx.db, gene.loc, seq.lens, pfam.gr = NULL, pfam.desc = NULL, 
pfam.ids = NULL, ...)

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.

tx.db

TranscriptDb object using the same reference genome as the contents of m.data

gene.loc

GRanges object containing gene data. It has HUGO gene symbols as names and has seqnames, ranges, and strand data for each entry.

seq.lens

Seqlengths for m.data, using the same reference genome as tx.db

pfam.gr

GRanges object of protein domain coordinates and Associated identifications

pfam.desc

list of PFAM definitions with Accession numbers

pfam.ids

character vector of Associated identifications with Accession numbers as names

...

Input objects from other databases, datasets, vectors describing plotting options. An example of possible input objects, using the human genome, are generated in mepHuman.

Details

The GUI window consists of two parts, a input selection menu and a notebook widget which displays m.data and the finished plots. Once selection is complete, all required inputs are processed and passed onto mutExonPlot. The GUI displays and saves many plots at once.

The text interface reads text entry from the user to complete input selection for plotting. The interface displays and saves one plot at a time.

See Also

mepHuman, mutExonPlot

Examples

## Not run: 
# library(TxDb.Hsapiens.UCSC.hg19.knownGene)
# 
# # Create a missense mutations dataset in TP53
# set.seed(1)
# locations = sample(7575000:7580000, size = 25)
# mut.df <- data.frame(chrom = "chr17", 
#                     start = locations, 
#                     end = locations, 
#                     strand = "-", 
#                     fill = letters[1:25])
# 
# # Generating sample data using TP53
# tx.db <- TxDb.Hsapiens.UCSC.hg19.knownGene
# seqs.hg19 <- seqlengths(tx.db)
# data(genesymbol, package = "biovizBase")
# 
# # Sample GRanges data with domains for P53
# sample <- GRanges(seqnames = "chr17", 
#                     IRanges(start = c(7576884, 7577499, 7579707), 
#                             end = c(7577102, 7579403, 7579899)), 
#                     strand = "-",
#                     domain = c("P53_tetramer", "P53", "P53_TAD"))
# 
# # Create PFAM objects
# objs <- makePFAMObjs()
# desc <- objs$desc
# ids <- objs$ids
# 
# int.opt <- c("Whole", "Custom")
# disp.opt <- c("All", "Reduce")
# dom.opt <- c("All", "Longest")
# 
# # GUI
# mepGUI(m.data = mut.df, tx.db = tx.db, gene.loc = genesymbol, 
#         seq.lens = seqs.hg19, pfam.desc = desc, pfam.ids = ids, 
#         pfam.gr = sample, int.opt = int.opt, disp.opt = disp.opt, 
#         dom.opt = dom.opt)
# 
# # Text Interface
# mepTxtInt(m.data = mut.df, tx.db = tx.db, gene.loc = genesymbol, 
#         seq.lens = seqs.hg19, pfam.desc = desc, pfam.ids = ids, 
#         pfam.gr = sample, int.opt = int.opt, disp.opt = disp.opt, 
#         dom.opt = dom.opt)
# ## End(Not run)