mddata: Prepare Quantities for Mean-Dispersion Plots Using ggplot2

In gu-mi/NBGOF: Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data

Description

This function prepares quantities for making mean-dispersion plots with curves of fitted negative binomial dispersion models. The result (a data frame) will be passed to the MDPlot function.

Usage

mddata(counts, x, model = NULL)

Arguments

counts	an m-by-n count matrix of non-negative integers. For a typical RNA-Seq experiment, this is the read counts with m genes and n samples
x	an n-by-p design matrix
model	a string of characters specifying the negative binomial dispersion model used to fit the data. Currently supported dispersion models include "NBP", "NBQ", "NBS", "STEP", "Common", "Tagwise-Common", "Tagwise-Trend" and "Trended"

Value

a data frame for each specified model.

gu-mi/NBGOF documentation built on Oct. 25, 2020, 3:30 a.m.