quickAssoc: Perform quick differential loop calling

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

Description

quickAssoc takes a loops object and performs a basic edgeR association on the counts matrix and groups from colData

Usage

quickAssoc(y)

## S4 method for signature 'loops'
quickAssoc(y)

Arguments

y	A loops object for association

Details

This function returns the output of fitting an edgeR model using the groups defined in colData for the specific loops object. The factor normalization is based on the edgeR model. For quick association, the number of groups is restricted to two. If a more complex group structure exists, consider using the loopAssoc function.

Value

A loops object

Examples

# Differential loop calling between naive and primed
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
np <- loops.small[,1:4]
assoc_np <- quickAssoc(np)

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