chipType: Determine ChIP-Seq Type of Protein Complex Binding

In tengmx/ComplexDiff: Differential Binding Estimation for Protein Complexes

Description

Estimate the types of protein complex binding. Protein complex binding might act similarly to normal transcription factors, where the changes are symmetrical between two biological conditions (unimodel on fold changes); or the changes might be globally one-side accompanied with some non-changing bindings (bimodel on fold changes). This function help to determine the binding type of given ChIP-Seq samples from two biological conditions using kernal density information of raw fold changes. As this function was designed to work on the raw counts (no normalization needed), only one replicate from each condition is allowed (input a two-column count matrix); otherwise, coverage difference acorss replicates might bias determination.

Usage

chipType(count, cutoff = 50L, fold = 10, h = 0.1, plot = TRUE)

Arguments

count	A two-column matrix of read counts or a SummarizedExperiment, where columns are samples and rows are peaks or high coverage bins. This object can be generated by function regionReads.
cutoff	A numeric cut off on count matrix. If positive, only peaks/bins with counts larger than cutoff in at least one sample are used to estimate the binding type. We recommend a larger cutoff since background signal can dramatically mask the right estimation of kernal density, especially for deep sequenced ChIP-seq samples. (Default: 50)
fold	A numeric threshold to help determine the binding type. In detail, if top two estimated modes on smoothed kernal density have a height differece less than the folds given by fold, binding type will be determined as bimodel; otherwise, it is unimodel. This number should be larger than 1. (Default: 10)
h	Initial smoothing factor when estimating kernal density of raw fold changes for bump hunting. (Default: 0.1)
plot	A logical indicator that if M-A plot and smoothed kernal density should be visualized. (Default: TRUE)

Value

A character with value either "bimodel" or "unimodel" to represent estimated binding type.

Examples

## load sample data
data(complex)
names(complex)

## test sample data
chipType(count=complex$counts)

tengmx/ComplexDiff documentation built on May 31, 2019, 8:34 a.m.