1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/simulate_3comp.R
\name{simulate_3comp}
\alias{simulate_3comp}
\title{Function to simulate three-component mixed cell line test data}
\usage{
simulate_3comp(
G1 = 675,
G2 = 25,
My = 20,
M1 = 100,
M2 = 100,
output.more.info = FALSE
)
}
\arguments{
\item{G1}{Number of genes, where \eqn{\mu_{N1}} is close to \eqn{\mu_{N2}}.}
\item{G2}{Number of genes, where \eqn{\mu_{N1}} is not close to
\eqn{\mu_{N2}}.}
\item{My}{Number of mixture tumor samples for simulation.}
\item{M1}{Number of first known reference for simulation.}
\item{M2}{Number of second known reference for simulation.}
\item{output.more.info}{The logical flag indicating wheter to show
True.data.T, True.data.N1 and True.data.N2 in the output. The default is
FALSE.}
}
\value{
\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, MuN2}) and unknown component
(\eqn{MuT}).} \item{Sigma}{Simulated \eqn{Sigma} of log2-normal distribution
for both known (\eqn{SigmaN1, SigmaN2}) and unknown component
(\eqn{SigmaT}).} \item{data.Y}{A SummarizedExperiment object of simulated
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 simulated
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{data.N2}{A SummarizedExperiment
object of expression data from additional reference samples. It is a \eqn{G}
by \eqn{M2} matrix where \eqn{G} is the number of genes and \eqn{M2} is the
number of samples for component 2.} \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 enabled only when
output.more.info = TRUE.} \item{True.data.N1}{A SummarizedExperiment object
of simulated true expression data for reference component 1 (e.g., stroma).
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 enabled only when
output.more.info = TRUE.} \item{True.data.N2}{A SummarizedExperiment object
of simulated true expression data for reference component 2 (e.g., immue).
It is a \eqn{G} by \eqn{M2} matrix where \eqn{G} is the number of genes and
\eqn{M2} is the number of samples for component 2. This is enabled only when
output.more.info = TRUE.}
}
\description{
Function to simulate three-component mixed cell line test data used in
DeMixT function.
}
\examples{
test.data = simulate_3comp(G1 = 675, G2 = 25, My = 20, M1 = 100, M2 = 100)
test.data$pi
test.data$Mu
test.data$Sigma
}
\keyword{simulate_3comp}
|
