TopDiffPeaks: Subset to top differentially accessible peaks for each...

In yanwu2014/chromfunks: Functions for Analyzing Chromatin Accessibility Data

Subset to top differentially accessible peaks for each cluster

Description

Subset to top differentially accessible peaks for each cluster

Usage

TopDiffPeaks(
  peaks_list,
  qval.cutoff = 0.05,
  specificity.cutoff = 0,
  logfc.cutoff = 0,
  dev.cutoff = 0,
  min.prop = 0,
  max.peaks = 30000,
  order.by = "qval"
)

Arguments

peaks_list	List of dA peak info per cluster. The output of CalcDiffAccess.
qval.cutoff	Q-value cutoff to call a site differentially accessible
specificity.cutoff	Specificity score cutoff
logfc.cutoff	Log fold-change cutoff
dev.cutoff	Minumum deviation above expected accessibility within the cluster
min.prop	Minimum fraction of cells in the cluster with the site accessible
max.peaks	Max number of peaks to keep for each cluster

Value

Filtered list of granges with cluster specificity, logfc, and p-value for each site tested

yanwu2014/chromfunks documentation built on Aug. 20, 2023, 9:17 a.m.