simulate.gaussian.peaks: simulate.gaussian.peaks

In helen-zhu/ConsensusPeaks: A Method for Peak Merging And Distribution Fitting Across Biological Replicates

Description

simulate.gaussian.peaks

Usage

## S3 method for class 'gaussian.peaks'
simulate(
  MU = 1,
  SD = 1,
  EXTEND.WIDTH = 50,
  NSAMPLES = 10,
  GENE,
  GTF = NULL,
  ANNOTATION = NULL,
  SEED = 123
)

Arguments

MU	An integer vector of means used to simulate a mixture of Gaussians. Values represent the mean bp, counted from the starting position of the transcript coordinate.
SD	An integer vector of standard deviations used to simulate a mixture of Gaussians. Units are in bp.
EXTEND.WIDTH	An integer vector of widths of peaks in bp.
NSAMPLES	An integer vector
GENE	The name of a gene in the GTF file on which to simulate peaks
GTF	The path to a GTF file used to simulate RNA peaks
SEED	A seed for reproducibility

Value

A data.frame in BED12 format, with an extra 'sample' column which can be used as input to ConsistentPeaks, PEAKS input

Examples

gtf.path = system.file("extdata", package = "ConsensusPeaks")
gtf = paste0(gtf.path, "/test.gtf")
simulate.gaussian.peaks(
MU = c(100, 150),
SD = c(10, 20),
EXTEND.WIDTH = c(50, 25),
NSAMPLES = c(10, 30),
GENE = "ENSGXX",
GTF = gtf,
SEED = 123
)

helen-zhu/ConsensusPeaks documentation built on Dec. 25, 2021, 9:39 a.m.