RepViz: Plot a genomic region

In RepViz: Replicate oriented Visualization of a genomic region

Description

Plot a genomic region

Usage

RepViz(region, genome = c("hg19", "hg38", "mm10"), BAM = NULL,
  BED = NULL, avgTrack = TRUE, geneTrack = TRUE, max = NULL,
  verbose = TRUE)

Arguments

region	a GRange object with chr, start, end
genome	a character vector 'hg19','hg38' or 'mm10'
BAM	a path to the BAM related csv input file
BED	a path to the BED related csv input file
avgTrack	a logical indicating if the average track should be included or not
geneTrack	a logical indicating if the gene track should be included or not
max	a numerical vector containing the yaxis maximum value of each BAM track
verbose	a logical indicating whether the progress of the plotting is shown

Value

displays the region specified by the user

Examples

region <- GRanges('chr12:110938000-110940000')
setwd(tempdir())
#Copying the files to the user working directory
file.copy(from = list.files(system.file('extdata', package = 'RepViz'), full.names = TRUE),
    to = tempdir())
#Generate the visualization of the given region
RepViz::RepViz(region = region,
    genome = 'hg19',
    BAM = 'BAM_input.csv',
    BED = 'BED_input.csv',
    avgTrack = TRUE,
    geneTrack = TRUE)

RepViz documentation built on Nov. 8, 2020, 8:07 p.m.