featureTest {diffloop} | R Documentation

## 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)

    ## S4 method for signature 'loops,GRanges'
    featureTest(x, features)

### Arguments

`x` | A loops object
`features` | A GRanges object defining regions for a combined test

### 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.

### Value

A data.frame sorted by FDR

### Examples

    # Human genes chromosome 1 regional association
    rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
    load(rda)
    # assoc <- loopAssoc(loops.small, coef = 2)
    # Gene based association
    # sw_jn <- featureTest(assoc, getHumanGenes(c('1')))

[Package diffloop version 1.12.0 Index]