diffloop (version 1.0.2)

featureTest: Combined association test for all loops in a defined region

Description

featureTest takes a loops and genomic coordinates of regions and computes combined significance metrics for each region using the Simes procedure

Usage

featureTest(x, features)
## S3 method for class 'loops,GRanges':
featureTest(x, features)

Arguments

x

A loops object

features

A GRanges object defining regions for a combined test

Value

• A data.frame sorted by FDR

Details

This function returns a data.frame sorted by FDR of each region. Assumes the region name is specified in the GRanges object with id column. Each feature is a one row in the GRanges object. The combined significance measure per feature is computed via the Simes method for intrachromosomal loops where at least one anchor from the loop overlaps with the region of interest.

Examples

# Human genes chromosome 1 regional association
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
jpn_loopfit <- loopFit(loops.small)
# Differential loop calling between naive and jurkat
assoc_jn <- loopTest(jpn_loopfit, coef = 2)
# Gene based association
sw_jn <- featureTest(assoc_jn, getHumanGenes(c('1')))