ExpandData: Expands a CNV input data frame for the maximum likelihood...

Description Usage Arguments Value Author(s) See Also

View source: R/ExpandData.R

Description

This function should be invisible to most users. The methods within CNV.fitModel require that the CNV data is expanded N times where N is the number of copies. This allows the use of Generalized Linear Models (GLM) in constraining the Gaussian mixture component locations and spreads to be functions of the copy number.

Usage

1
ExpandData(batch, trait, names, signal, ncomp, association.strata = NULL)

Arguments

batch

List of vectors, one vector per batch in the data. Because each element in the list corresponds to a batch, each element should be a vector with a unique values repeated as many times as the number of data point in the batch.

trait

List of vectors, one vector per batch in the data. Each element of the list can be either a vector of quantitative traits or a vector of 0 and 1 in a case/control framework

names

List of vectors, one vector per batch in the data containing names for each data point, typically individual IDs.

signal

List, one vector per batch in the data.

ncomp

Integer, number of components one wants to fit to the data

association.strata

Optional, a factor vector containing the strata when using a stratified test of association.

Value

An expanded data frame needed for CNVfit.binary.

Author(s)

Vincent Plagnol [email protected] and Chris Barnes [email protected]

See Also

CNVtest.binary


CNVtools documentation built on Nov. 1, 2018, 2:24 a.m.