do.aGFF.calc {ACME} | R Documentation

## Perform ACME calculation

### Description

This function performs the moving window chi-square calculation. It is written in C, so is quite fast.

### Usage

    do.aGFF.calc(x, window, thresh)

### Arguments

`x` | An `aGFF` class object
`window` | An integer value, representing the number of basepairs to include in the windowed chi-square calculation
`thresh` | The quantile of the data distribution for each sample that will be used to classify a probe as positive

### Details

A window size on the order of 2-3 times the average size of fragments from sonication, digestion, etc. and containing at least 8-10 probes is the recommended size. Larger size windows are probably more sensitive, but obviously reduce the accuracy with which boundaries of signal can be called.

A threshold of between 0.9 and 0.99 seems empirically to be adequate. If one plots the histogram of data values and there is an obvious better choice (such as a bimodal distribution, with one peak representing enrichment), a more data-driven approach may yield better results.

### Value

An object of class `aGFFCalc`

### Author(s)

Sean Davis <sdavis2@mail.nih.gov>

### Examples

    data(example.agff)
    example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
    example.agffcalc

[Package ACME version 2.48.0 Index]