do.aGFF.calc: Perform ACME calculation

In ACME: Algorithms for Calculating Microarray Enrichment (ACME)

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 <[e-mail]>

Examples

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

ACME documentation built on Nov. 8, 2020, 7:51 p.m.