loopAssoc {diffloop} | R Documentation

## Generalized differential Loop Calling

### Description

`loopAssoc` takes a `loops` object and prepares it for the returns another `loops` object with summary statistics per-loop in the `rowData`

### Usage

    loopAssoc(y, method = "edgeR", design = NULL, coef = NULL,
      contrast = NULL)

    ## S4 method for signature 'loops'
    loopAssoc(y, method = "edgeR", design = NULL,
      coef = NULL, contrast = NULL)

### Arguments

`y` | A loops object for association
`method` | Specifies association; either "Voom" or "edgeR"
`design` | A design matrix of the samples; required for "Voom"
`coef` | A vector for the coefficient of GLM. See edgeR manual
`contrast` | A vector for the contrast. See edgeR manual

### Details

By the default, we generate is to generate a design matrix from `loops@colData$groups`. Currently, 'edgeR' and 'Voom' are the two supported association methods, but new association tests may be added in later developments.

### Value

A loops object

### Examples

    # Differential loop fit
    rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
    load(rda)
    # assoc <- loopAssoc(loops.small, coef = 2)

[Package diffloop version 1.12.0 Index]