Plotting Saturation curves — saturationPlot • ATACseqQC

Plotting the saturation curves.

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

Haibo Liu

Examples

if(interactive()){
}