loopAssoc: Generalized differential Loop Calling

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

loopAssoc takes a loops object and prepares it for the returns another loops object with summary statistics per-loop in the rowData

Usage

loopAssoc(y, method = "edgeR", design = NULL, coef = NULL,
  contrast = NULL)

## S4 method for signature 'loops'
loopAssoc(y, method = "edgeR", design = NULL,
  coef = NULL, contrast = NULL)

Arguments

y	A loops object for association
method	Specifies association; either "Voom" or "edgeR"
design	A design matrix of the samples; required for "Voom"
coef	A vector for the coefficient of GLM. See edgeR manual
contrast	A vector for the contrast. See edgeR manual

Details

By the default, we generate is to generate a design matrix from loops@colData$groups. Currently, 'edgeR' and 'Voom' are the two supported association methods, but new association tests may be added in later developments.

Value

A loops object

Examples

# Differential loop fit
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
# assoc <- loopAssoc(loops.small, coef = 2)

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.