simulate_3comp: Function to simulate three-component mixed cell line test...

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

Function to simulate three-component mixed cell line test data

Description

Function to simulate three-component mixed cell line test data used in DeMixT function.

Usage

simulate_3comp(
  G1 = 675,
  G2 = 25,
  My = 20,
  M1 = 100,
  M2 = 100,
  output.more.info = FALSE
)

Arguments

G1	Number of genes, where \mu_{N1} is close to \mu_{N2}.
G2	Number of genes, where \mu_{N1} is not close to \mu_{N2}.
My	Number of mixture tumor samples for simulation.
M1	Number of first known reference for simulation.
M2	Number of second known reference for simulation.
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

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.
Mu	Simulated Mu of log2-normal distribution for both known (MuN1, MuN2) and unknown component (MuT).
Sigma	Simulated Sigma of log2-normal distribution for both known (SigmaN1, SigmaN2) and unknown component (SigmaT).
data.Y	A SummarizedExperiment object of simulated expression data from mixed tumor samples. It is a G by My matrix where G is the number of genes and My is the number of mixed samples. Samples with the same tissue type should be placed together in columns.
data.N1	A SummarizedExperiment object of simulated expression data from reference component 1 (e.g., normal). It is a G by M1 matrix where G is the number of genes and M1 is the number of samples for component 1.
data.N2	A SummarizedExperiment object of expression data from additional reference samples. It is a G by M2 matrix where G is the number of genes and M2 is the number of samples for component 2.
True.data.T	A SummarizedExperiment object of simulated tumor expression data. It is a G by My matrix, where G is the number of genes and My is the number of mixed samples.This is enabled only when output.more.info = TRUE.
True.data.N1	A SummarizedExperiment object of simulated true expression data for reference component 1 (e.g., stroma). It is a G by M1 matrix where G is the number of genes and M1 is the number of samples for component 1. This is enabled only when output.more.info = TRUE.
True.data.N2	A SummarizedExperiment object of simulated true expression data for reference component 2 (e.g., immue). It is a G by M2 matrix where G is the number of genes and M2 is the number of samples for component 2. This is enabled only when output.more.info = TRUE.

Examples

test.data = simulate_3comp(G1 = 675, G2 = 25, My = 20, M1 = 100, M2 = 100)
test.data$pi
test.data$Mu
test.data$Sigma

wwylab/DeMixT documentation built on July 17, 2024, 9:14 p.m.