The soggi function and ChIPprofile object.

Description

Manual for soggi and ChIPprofile object

The soggi function is the constructor for ChIPprofile objects.

Usage

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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

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