quickAssocVoom: Perform quick differential loop calling

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

Description

quickAssocVoom takes a loops object and performs a basic voom association on the counts matrix and groups from colData

Usage

quickAssocVoom(y)

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

Arguments

y	A loops object for association

Details

This function returns the output of fitting an voom model using the groups defined in colData for the specific loops object. The factor normalization is based on the voom 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_voom <- quickAssocVoom(np)

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