ChIPprofile-class {soGGi} | R Documentation

## The soggi function and ChIPprofile object.

### 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

[Package soGGi version 1.26.0 Index]