ConsensusPeaks: ConsensusPeaks: A wrapper for peak merging functions

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

Description

ConsensusPeaks: A wrapper for peak merging functions

Usage

ConsensusPeaks(
  GENES = "all",
  PEAKS,
  RNA.OR.DNA = c("rna", "dna"),
  METHOD = c("dpc", "hmm"),
  GTF = NULL,
  DP.RESOLUTION = 50,
  DP.ITERATIONS = 1000,
  DP.WEIGHT.THRESHOLD = 0.2,
  DP.N.SD = 1,
  DP.ALPHA.PRIORS = c(1, 2),
  DP.SEED = 123,
  PLOT.MERGED.PEAKS = F,
  OUTPUT.TAG = "",
  OUTPUTDIR = ".",
  WRITE.OUTPUT = T,
  DIAGNOSTIC = F,
  FIT.MIXTURE = T,
  ANNOTATION = NULL
)

Arguments

GENES	A character vector of genes to be tested
PEAKS	A data frame containing the following columns, and potentially extras, usually found in a BED12 file, base 0 system chr chromosomes, character, same format as those identified in GTF file start starting position of the peak, integer. base 0 end end position of the peak, integer, base 0 name gene id, character score p-value associated with the peak strand strand of the gene, only +, -, * are accepted blockCount number of segments in the peak, integer blockSizes size of segments in the peak, BED12 notation, comma-separated blockStarts starting positions of segments, BED12 notation, comma-separated sample sample_id of samples, character
RNA.OR.DNA	One of 'rna' or 'dna' indicating whether peaks are identified on the transcriptome or genome
METHOD	One 'dpc', 'union', 'corces' dpc A GMM is fitted on the peaks using a Dirichlet process prior union The union of overlapping peaks is reported coerces A 'daisy chain' model described in Coerces et al., 2012, Science, where the most statistically significant peak is chosen
GTF	The path to a GTF file, character string.
DP.RESOLUTION	If the METHOD is 'dpc', specify the resolution of the provided PEAKS data.frame. This usually corresponds to the bin width chosen when the peaks are called, a positive integer.
DP.ITERATIONS	If the METHOD is 'dpc', specify the number of iterations used to fit the GMM, a positive integer.
DP.WEIGHT.THRESHOLD	If the METHOD is 'dpc', specify the minimum weight used to threshold the Gaussians. This value is required to be numeric and between 0 and 1.
DP.N.SD	If the METHOD is 'dpc', specify the standard deviation of the Gaussians required to identify peak boundaries, numeric value, above 0.
DP.ALPHA.PRIORS	If the METHOD is 'dpc', specify the priors (alpha, beta) for the Gamma distribution from which the weight concentration prior is drawn, numeric vector of length 2
DP.SEED	A seed for reproducibility, integer above 0.
PLOT.MERGED.PEAKS	Either a logical value (TRUE or FALSE) indicating all or none of the merged peaks should be plotted. Otherwise, a character vector of genes whose merged peaks should be plotted.
OUTPUT.TAG	A character string added to the names of any output files.
OUTPUTDIR	Output directory. If the directory does not exist, ConsensusPeaks will attempt to create the directory.
WRITE.OUTPUT	A logical value indicating whether the output table should be written.
ANNOTATION

Value

A data frame with the same columns as 'PEAKS' indicating the coordinates of the merged peaks in genomic coordinates. If the method is 'dpc', additional columns with the sample names of the samples will indicate the merged p-value using Fisher's Method.

Examples

data.path = system.file("extdata", package = "ConsensusPeaks")
gtf = paste0(data.path, "/test.gtf")
peaks.file = paste0(data.path, "/peaks.bed")
peaks = read.table(peaks.file, header = F, sep = '\t', stringsAsFactors = F)
colnames(peaks) = c("chr", "start", "end", "name", "score", "strand", "thickStart", "thickEnd", "itemRGB", "blockCount", "blockSizes", "blockStarts", "sample")

results = ConsensusPeaks(
GENES = c("ENSGXX", "ENSGYY"),
PEAKS = peaks,
RNA.OR.DNA = "rna",
METHOD = "dpc",
GTF = gtf,
DP.RESOLUTION = 10,
DP.ITERATIONS = 1000,
DP.WEIGHT.THRESHOLD = 0.1,
DP.N.SD = 1.5,
DP.ALPHA.PRIORS = c(0.5,5),
DP.SEED = 123,
PLOT.MERGED.PEAKS = F,
OUTPUT.TAG = "TEST",
OUTPUTDIR = ".",
WRITE.OUTPUT = F)

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