DPDE4PM: DPDE4PM merged RNA-seq peaks called on different samples

In helen-zhu/DPDE4PM: A Method for Peak Merging Across Biological Replicates

Description

DPDE4PM merged RNA-seq peaks called on different samples

Usage

DPDE4PM(
  GENE,
  PEAKS,
  GTF = NULL,
  ANNOTATION = NULL,
  RESOLUTION = 50,
  DP.ITERATIONS = 1000,
  WEIGHT.THRESHOLD = 0.2,
  N.SD = 1,
  OUTPUTDIR = ".",
  PLOT.RESULT = F,
  WRITE.OUTPUT = T,
  OUTPUT.TAG = "",
  ALPHA.PRIORS = c(1, 2),
  SEED = 123
)

Arguments

GENE	A 'character' gene id corresponding to the gene_id's found in the GTF files and the 'name' column in the peak files
PEAKS	A data frame containing the following columns, and potentially extras, usually found in a BED12 file, base 0 system chr chromosomes, same as in GTF file start starting position of the peak, base 0 end end position of the peak, base 0 name gene id score p-value associated with the peak strand strand of the gene blockCount number of segments in the peak blockSizes size of segments in the peak, BED12 notation blockStarts starting positions of segments, BED12 notation sample sample_id of samples
GTF	The GTF file used to generate the peaks. This is used to determine the genomic coordinates of the gene.
ANNOTATION	A object created by the read.gtf function. This allows the user to provide an annotation object to save compute time during parallelization.
RESOLUTION	The width (bps) used to sample points from the peaks. This is likely optimized by choosing the window size used to generate the peaks.
DP.ITERATIONS	Number of iterations used to fit the Dirichlet Process
WEIGHT.THRESHOLD	A proportion (out of 1) used to determine the percentage of data accounted for by the GMM to be called a peak
N.SD	Number of standard deviations from the mean for each fitted Gaussian that should considered part of the joint peak
OUTPUTDIR	Output directory
PLOT.RESULT	TRUE or FALSE, whether plots should be generated
WRITE.OUTPUT	TRUE or FALSE, whether an output file should be saved
OUTPUT.TAG	A character string indicating a tag to track the generated files
ALPHA.PRIORS	A length 2 numeric vector indicating alpha, beta of the Gamma distribution from which the concentration weight parameter alpha is drawn, see the R package dirichletprocess
SEED	a seed for reproducibility

Value

A dataframe with BED12 columns and additional columns for each sample in the PEAKS dataframe and associated p-value with that peak.

helen-zhu/DPDE4PM documentation built on Feb. 17, 2021, 9:46 a.m.