Usage
regionPlot(bamFile, testRanges, samplename = NULL, nOfWindows = 100, FragmentLength = 150, style = "point", distanceAround = NULL, distanceUp = NULL, distanceDown = NULL, distanceInRegionStart = NULL, distanceOutRegionStart = NULL, distanceInRegionEnd = NULL, distanceOutRegionEnd = NULL, paired = FALSE, normalize = "RPM", plotBy = "coverage", removeDup = FALSE, verbose = TRUE, format = "bam", seqlengths = NULL, forceFragment = NULL, method = "bin", genome = NULL, cutoff = 80, downSample = NULL, minFragmentLength = NULL, maxFragmentLength = NULL)
Arguments
bamFile
Character vector for location of BAM file or bigWig, an rleList or PWM matrix.
testRanges
GRanges object or character vector of BED file location of regions to plot.
samplename
Character vector of sample name. Default is NULL.
nOfWindows
Number of windows to bin regions into for coverage calculations (Default 100)
FragmentLength
Integer vector Predicted or expected fragment length.
style
"Point" for per base pair plot, "percentOfRegion" for normalised length and "region" for combined plot
distanceAround
Distance around centre of region to be used for plotting
distanceUp
Distance upstream from centre of region to be used for plotting
distanceDown
Distance downstream from centre of region to be used for plotting
distanceInRegionStart
Distance into region start
(5' for Watson/positive strand or notspecified strand Regions,3' for Crick/negatie strand regions)
for plotting.
distanceOutRegionStart
Distance out from region start
(5' for Watson/positive strand or notspecified strand Regions,3' for Crick/negatie strand regions)
for plotting.
distanceInRegionEnd
Distance into region end
(3' for Watson/positive strand or notspecified strand Regions,5' for Crick/negatie strand regions)
for plotting.
distanceOutRegionEnd
Distance out from region end
(3' for Watson/positive strand or notspecified strand Regions,5' for Crick/negatie strand regions)
for plotting.
normalize
Calculate coverage as RPM. Presently only RPM available.
plotBy
Score to be used for plotting. Presently only coverage.
removeDup
Remove duplicates before calculating coverage.
format
character vector of "bam", "bigwig", "RleList" or "PWM"
seqlengths
Chromosomes to be used. If missing will report all.
forceFragment
Centre fragment and force consistent fragment width.
method
Character vector of value "bp","bin" or "spline".
The bin method divides a region of interest into equal sized bins of number specified in nOfWindows.
Coverage or counts are then summarised within these windows.
The spline method creates a spline with the number of spline points as specified in nOfWindows argument.
genome
BSGenome object to be used when using PWM input.
cutoff
Cut-off for idnetifying motifs when using PWM input.
downSample
Down sample BAM reads to this proportion of orginal.
minFragmentLength
Remove fragments smaller than this.
maxFragmentLength
Remove fragments larger than this.