saturationPlot: Plotting Saturation curves
In jianhong/ATACseqQC: ATAC-seq Quality Control

saturationPlot

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.