DeMixT | R Documentation |
DeMixT is a software that performs deconvolution on transcriptome data from a mixture of two or three components.
DeMixT(
data.Y,
data.N1,
data.N2 = NULL,
niter = 10,
nbin = 50,
if.filter = TRUE,
filter.sd = 0.5,
ngene.selected.for.pi = NA,
mean.diff.in.CM = 0.25,
nspikein = NULL,
gene.selection.method = "GS",
ngene.Profile.selected = NA,
tol = 10^(-5),
output.more.info = FALSE,
pi01 = NULL,
pi02 = NULL,
nthread = parallel::detectCores() - 1
)
data.Y |
A SummarizedExperiment object of expression data from mixed
tumor samples. It is a |
data.N1 |
A SummarizedExperiment object of expression data
from reference component 1 (e.g., normal). It is a |
data.N2 |
A SummarizedExperiment object of expression data from
additional reference samples. It is a |
niter |
The maximum number of iterations used in the algorithm of iterated conditional modes. A larger value better guarantees the convergence in estimation but increases the running time. The default is 10. |
nbin |
The number of bins used in numerical integration for computing complete likelihood. A larger value increases accuracy in estimation but increases the running time, especially in a three-component deconvolution problem. The default is 50. |
if.filter |
The logical flag indicating whether a predetermined filter rule is used to select genes for proportion estimation. The default is TRUE. |
filter.sd |
The cut-off for the standard deviation of lognormal distribution. Genes whose log transferred standard deviation smaller than the cut-off will be selected into the model. The default is 0.5. |
ngene.selected.for.pi |
The percentage or the number of genes used for
proportion estimation. The difference between the expression levels from
mixed tumor samples and the known component(s) are evaluated, and the most
differential expressed genes are selected, which is called DE. It is enabled
when if.filter = TRUE. The default is |
mean.diff.in.CM |
Threshold of expression difference for selecting genes in the component merging strategy. We merge three-component to two-component by selecting genes with similar expressions for the two known components. Genes with the mean differences less than the threshold will be selected for component merging. It is used in the three-component setting, and is enabled when if.filter = TRUE. The default is 0.25. |
nspikein |
The number of spikes in normal reference used for proportion
estimation. The default value is |
gene.selection.method |
The method of gene selection used for proportion estimation. The default method is 'GS', which applies a profile likelihood based method for gene selection. If it is set to 'DE', the most differential expressed genes are selected. |
ngene.Profile.selected |
The number of genes used for proportion
estimation ranked by profile likelihood. The default is
|
tol |
The convergence criterion. The default is 10^(-5). |
output.more.info |
The logical flag indicating whether to show the estimated proportions in each iteration in the output. |
pi01 |
Initialized proportion for first kown component. The default is
|
pi02 |
Initialized proportion for second kown component. pi02 is needed
only for running a three-component model. The default is |
nthread |
The number of threads used for deconvolution when OpenMP is available in the system. The default is the number of whole threads minus one. In our no-OpenMP version, it is set to 1. |
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, and each column corresponds to one sample. |
pi.iter |
Estimated proportions in each iteration. It is a |
ExprT |
A matrix of deconvolved expression profiles corresponding to T-component in mixed samples for a given subset of genes. Each row corresponds to one gene and each column corresponds to one sample. |
ExprN1 |
A matrix of deconvolved expression profiles corresponding to N1-component in mixed samples for a given subset of genes. Each row corresponds to one gene and each column corresponds to one sample. |
ExprN2 |
A matrix of deconvolved expression profiles corresponding to N2-component in mixed samples for a given subset of genes in a three-component setting. Each row corresponds to one gene and each column corresponds to one sample. |
Mu |
A matrix of estimated |
Sigma |
Estimated |
gene.name |
The names of genes used in estimating the proportions. If no gene names are provided in the original data set, the genes will be automatically indexed. |
Zeya Wang, Wenyi Wang
Wang Z, Cao S, Morris J S, et al. Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration. iScience, 2018, 9: 451-460.
http://bioinformatics.mdanderson.org/main/DeMixT
# Example 1: simulated two-component data by using GS(gene selection method)
data(test.data.2comp)
# res <- DeMixT(data.Y = test.data.2comp$data.Y,
# data.N1 = test.data.2comp$data.N1,
# data.N2 = NULL, nspikein = 50,
# gene.selection.method = 'GS',
# niter = 10, nbin = 50, if.filter = TRUE,
# ngene.selected.for.pi = 150,
# mean.diff.in.CM = 0.25, tol = 10^(-5))
# res$pi
# head(res$ExprT, 3)
# head(res$ExprN1, 3)
# head(res$Mu, 3)
# head(res$Sigma, 3)
#
# Example 2: simulated two-component data by using DE(gene selection method)
# data(test.data.2comp)
# res <- DeMixT(data.Y = test.data.2comp$data.Y,
# data.N1 = test.data.2comp$data.N1,
# data.N2 = NULL, nspikein = 50, g
# ene.selection.method = 'DE',
# niter = 10, nbin = 50, if.filter = TRUE,
# ngene.selected.for.pi = 150,
# mean.diff.in.CM = 0.25, tol = 10^(-5))
#
# Example 3: three-component mixed cell line data applying
# component merging strategy
# data(test.data.3comp)
# res <- DeMixT(data.Y = test.data.3comp$data.Y,
# data.N1 = test.data.3comp$data.N1,
# data.N2 = test.data.3comp$data.N2,
# if.filter = TRUE)
#
# Example: convert a matrix into the SummarizedExperiment format
# library(SummarizedExperiment)
# example <- matrix(c(1, 2, 3, 4, 5, 6), nrow = 2, ncol = 3, byrow = TRUE)
# example.se <- SummarizedExperiment(assays = list(counts = example))
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