getQ: Estimate the shrinkage target based on the quantiles of initial targets

Description

The shrinkage target is estimated.

Usage

getQ(countsTable, sizeFactors=NULL, q.vec=NULL, plotASD=FALSE,  numPart=1, propForSigma=c(0, 1), verbose=TRUE, shrinkTarget=NULL,  shrinkQuantile=NULL)

Arguments

countsTable

A data.frame or a matrix of counts in which a row represents for a gene and a column represents for a sample. There must be at least two columns in countsTable.

sizeFactors

A vector of values around 1 which are used to normalize between samples or libraries. The length of this vector equals to the number of columns in countsTable.

q.vec

A vector of sequence defines the quantiles. When q.vec=NULL, this function will generate a sequence for q.vec using seq(0.05, 0.995, 0.005).

plotASD

A logic value. If plotASD=TRUE, then the plot of ASD versus target points will be drawn. The SH estimates are obtained by shrinking the MM estimates toward a target point. Different SH estimates are generated using different target points. The target point that helps produce a small and stable averaged squared difference (ASD) between the MM estimates and the SH estimates is the point that approximates the common information across per- gene dispersion.

numPart

An integer indicates the number of groups for dispersion estimation. `numPart=1' is the default value. It assumes that most of the genes share one point of stabilization (POS), and calculates the SH estimates without separating data into groups. When we assumes that genes can share different targets, the grouped SH estimates on dispersion can be be utilized. In this situation, users need to provide a number indicating the number of POS.

propForSigma

A range vector between 0 and 1 that is used to select a subset of data. It helps users to make a flexible choice on the subset of data when they believe only part of data should be used to estimate the variation among per-gene dispersion. A default input propForSigma=c(0, 1) is recommended. It means that we want to use all the data to estimate the variation.

verbose

A logic value. When verbose=TRUE, the detail information will be printed in the console.

shrinkTarget

A value for the shrinkage target of dispersion estimates. If ``shrinkTarget=NULL" and ``shrinkQuantile" is a value instead of NULL, then the quantile value for ``shrinkQuantile" is converted into the scale of dispersion estimates and used as the target. If both of them are NULL, then a value that is small and minimizes the average squared difference is automatically used as the target value. If both of them are not NULL, then the value of ``shrinkTarget" is used as the target.

shrinkQuantile

A quantile value for the shrinkage target of dispersion estimates. If ``shrinkTarget=NULL" and ``shrinkQuantile" is a value instead of NULL, then the quantile value for ``shrinkQuantile" is converted into the scale of dispersion estimates and used as the target. If both of them are NULL, then a value that is small and minimizes the average squared difference is automatically used as the target value. If both of them are not NULL, then the value of ``shrinkTarget" is used as the target.

Value

target: The estimated point for stabilization that represents the common in formation across per-gene dispersion.
q: A value that shows the quantile of the target value across per-gene dispersion.

Examples

Run this code

#load a simulated data that includes a count table
data("countsTable")
conds <- c("A",  "B")
getQ(countsTable, plotASD=TRUE)

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