ChIPprofile: The soggi function and ChIPprofile object.

In ThomasCarroll/soGGi: Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

Description

Manual for soggi and ChIPprofile object

The soggi function is the constructor for ChIPprofile objects.

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.
paired	Is data paired end
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.
verbose	TRUE or FALSE
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.
downSample	Down sample BAM reads to this proportion of orginal.
genome	BSGenome object to be used when using PWM input.
cutoff	Cut-off for idnetifying motifs when using PWM input.
minFragmentLength	Remove fragments smaller than this.
maxFragmentLength	Remove fragments larger than this.

Value

ChIPprofile A ChIPprofile object.

References

See http://bioinformatics.csc.mrc.ac.uk for more details on soGGi workflows

Examples

data(chipExampleBig)
chipExampleBig

ThomasCarroll/soGGi documentation built on May 7, 2019, 8:40 a.m.