chromfunks: Functions for Analyzing Chromatin Accessibility Data

FindCausalPeaks

R Documentation

Identify most impactful SNPs for a given trait/cell type combo

Description

Identify most impactful SNPs for a given trait/cell type combo

Usage

FindCausalPeaks(
  SE,
  traits,
  bg.peaks = NULL,
  min.z = 1,
  min.PP = 0.025,
  return.mat = F
)

Arguments

`SE`	Accessibility counts as a Summarized Experiment object
`traits`	Posterior probability score of each peak for every trait as a Summarized Experiment object
`bg.peaks`	Matrix of background peaks. Will be computed with getBackgroundPeaks if not specified
`min.z`	Z-score cutoff for peaks
`min.PP`	Posterior probability score for peaks
`return.mat`	Return all z-scores

Value

List of lists of causal peaks for each trait and cell type. Each trait/cell type pair has a dataframe with the z-score, accessibility deviation, and posterior probability for each causal peak

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