R/test.data.2comp.R

In DeMixT: Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

#' @title Simulated two-component test data
#' 
#' @description A list of simulated two-component test data used in 
#' DeMixT function. Expression data with 500 genes and 100 samples 
#' are simulated.
#' 
#' @return A list with 5 elements (2 more elements when output.more.info = 
#' TRUE), which are
#' \item{pi}{A matrix of estimated proportion. First row and second row 
#' corresponds to the proportion estimate for the known components and unkown 
#' component respectively for two or three component settings. Each column 
#' corresponds to one sample.}
#' \item{Mu}{Simulated \eqn{Mu} of log2-normal distribution for both known
#' (\eqn{MuN1}) and unknown component (\eqn{MuT}).}
#' \item{Sigma}{Simulated \eqn{Sigma} of log2-normal distribution for both 
#' known (\eqn{SigmaN1}) and unknown component (\eqn{SigmaT}).}
#' \item{data.Y}{A SummarizedExperiment object of expression data from mixed 
#' tumor samples. It is a \eqn{G} by \eqn{My} matrix where \eqn{G} is the number
#' of genes and \eqn{My} is the number of mixed samples. Samples with the same
#' tissue type should be placed together in columns.}
#' \item{data.N1}{A SummarizedExperiment object of expression data 
#' from reference component 1 (e.g., normal). It is a \eqn{G} by \eqn{M1} matrix 
#' where \eqn{G} is the number of genes and \eqn{M1} is the number of samples 
#' for component 1.} 
#' \item{True.data.T}{A SummarizedExperiment object of simulated tumor expression 
#' data. It is a \eqn{G} by \eqn{My} matrix, where \eqn{G} is the number of 
#' genes and \eqn{My} is the number of mixed samples. This is shown only when 
#' output.more.info = TRUE.}
#' \item{True.data.N1}{A SummarizedExperiment object of simulated true 
#' expression data for reference component 1 (e.g., normal). It is a \eqn{G} 
#' by \eqn{M1} matrix where \eqn{G} is the number of genes and \eqn{M1} is the 
#' number of samples for component 1. This is shown only when 
#' output.more.info = TRUE.}
'test.data.2comp'