diffloop (version 1.0.2)

quickAssoc: Perform quick differential loop calling

Description

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

Usage

quickAssoc(y)
## S3 method for class 'loops':
quickAssoc(y)

Arguments

y

A loops object for association

Value

• A loops object

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 loopFit and loopTest functions

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)