saturationPlot {ATACseqQC} | R Documentation

## Plotting Saturation curves

### Description

Plotting the saturation curves.

### Usage

    saturationPlot(
      subsamplingPeakFiles,
      subsamplingSizes,
      sep = "\t",
      header = FALSE,
      fdr = 0.05,
      fdrCol = 9,
      startCol = 2,
      endCol = 3,
      skipLines = 1,
      peakCaller = "MACS2",
      outPrefix,
      span = 2,
      degree = 2
    )

### Arguments

`subsamplingPeakFiles` | A character vector containing peak files from peak calling tools, such as MACS2. Currently only MACS2 output is supported.
`subsamplingSizes` | A named vector of integers, which are the sizes of subsamples for peak calling. The names of subsamplingPeakFiles should be identical to the basenames of subsamplingPeakFiles.
`sep` | A character vector of length 1L, which is the column separator used in peak files.
`header` | A boolean (TRUE or FASLE) vector of length 1L, showing whether there are column headers in the peak files.
`fdr` | A decimal between 0 and 1, a cutoff of statistical significance of peak detection.
`fdrCol` | An integer, column index for fdr.
`startCol` | An integer, column index for start positions of peak regions.
`endCol` | An integer, column index for end positions of peak regions.
`skipLines` | An integer, the number of lines (comments or instruction) to skip when peak files are read into R.
`peakCaller` | A character vector of length 1L contatining the name of the peak caller used to generate the peak files, such as "MACS2". Currently only MACS2 output (XXX.narrowPeak or XXX.broadPeak) is support.
`outPrefix` | A character vector of length 1L, the file prefix for outputting saturation plots.
`span` | An integer, the span parameter for loess smoothing to fit a smoothed saturation curve.
`degree` | An integer, the degree of local polynomial used for loess.

### Value

A data frame of three columns: subsamplingSizes, the number of subsampled fragments; numPeaks, the number of peaks with fdr less than a given threshold when a given number of fragmetns are subsampled; breadth, the total breadth of peaks with fdr less than a given threshold for give subsampling when a given number of fragmetns are subsampled.

### Author(s)

Haibo Liu

### Examples

    if(interactive()){
    }

[Package ATACseqQC version 1.11.8 Index]