StromaExp: Stroma (Immune) Component Gene Expression Estimation

In DisHet: Estimate the Gene Expression Levels and Component Proportions of the Normal, Stroma (Immune) and Tumor Components of Bulk Tumor Samples

Description

This function estimate the stroma component gene expression profiles of all patients, using the proportion estimates obtained from function DisHet. The estimates are stored in a p-by-k matrix, where p is the number of genes and k is the number of patients.The order of genes and the order of patients are the same as in the input bulk sample expression matrix.

Usage

StromaExp(exp_T,exp_N,exp_G, rho)

Arguments

exp_T	Gene expression in bulk RNA-seq samples. The rows correspond to different genes. The columns correspond to different patients.
exp_N	Gene expression in the corresponding normal samples. The rows list the same set of genes as in exp_G. The columns correspond to patients matched with exp_T.
exp_G	Gene expression in the corresponding tumor samples. The rows list the same set of genes as in exp_G. The columns correspond to patients matched with exp_T.
rho	Output from function DisHet: the patient-specific proportion estimates corresponding to tumor, normal, stroma components in order.

Examples

  load(system.file("example/example_data.RData",package="DisHet"))
  exp_T <- exp_T[1:200,]
  exp_N <- exp_N[1:200,]
  exp_G <- exp_G[1:200,]
  
  rho <- DisHet(exp_T, exp_N, exp_G, save=FALSE, n_cycle=200, mean_last=50)
  S <- StromaExp(exp_T,exp_N,exp_G, rho)

Example output

Loading required package: gtools
Loading required package: matrixStats
  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.05 
Finished iteration 1 


  Overall acceptance rate for S: 0.78 
  Overall acceptance rate for rho: 0.13 
Finished iteration 2 


  Overall acceptance rate for S: 0.75 
  Overall acceptance rate for rho: 0.12 
Finished iteration 3 


  Overall acceptance rate for S: 0.75 
  Overall acceptance rate for rho: 0.19 
Finished iteration 4 


  Overall acceptance rate for S: 0.7 
  Overall acceptance rate for rho: 0.09 
Finished iteration 5 


  Overall acceptance rate for S: 0.68 
  Overall acceptance rate for rho: 0.17 
Finished iteration 6 


  Overall acceptance rate for S: 0.64 
  Overall acceptance rate for rho: 0.11 
Finished iteration 7 


  Overall acceptance rate for S: 0.69 
  Overall acceptance rate for rho: 0.09 
Finished iteration 8 


  Overall acceptance rate for S: 0.69 
  Overall acceptance rate for rho: 0.04 
Finished iteration 9 


  Overall acceptance rate for S: 0.67 
  Overall acceptance rate for rho: 0.09 
Finished iteration 10 


  Overall acceptance rate for S: 0.68 
  Overall acceptance rate for rho: 0.09 
Finished iteration 11 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.13 
Finished iteration 12 


  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.13 
Finished iteration 13 


  Overall acceptance rate for S: 0.66 
  Overall acceptance rate for rho: 0.1 
Finished iteration 14 


  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.19 
Finished iteration 15 


  Overall acceptance rate for S: 0.64 
  Overall acceptance rate for rho: 0.22 
Finished iteration 16 


  Overall acceptance rate for S: 0.63 
  Overall acceptance rate for rho: 0.22 
Finished iteration 17 


  Overall acceptance rate for S: 0.63 
  Overall acceptance rate for rho: 0.22 
Finished iteration 18 


  Overall acceptance rate for S: 0.56 
  Overall acceptance rate for rho: 0.13 
Finished iteration 19 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.17 
Finished iteration 20 


  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.22 
Finished iteration 21 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.17 
Finished iteration 22 


  Overall acceptance rate for S: 0.6 
  Overall acceptance rate for rho: 0.17 
Finished iteration 23 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.22 
Finished iteration 24 


  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.17 
Finished iteration 25 


  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.17 
Finished iteration 26 


  Overall acceptance rate for S: 0.6 
  Overall acceptance rate for rho: 0.17 
Finished iteration 27 


  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.18 
Finished iteration 28 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.13 
Finished iteration 29 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.18 
Finished iteration 30 


  Overall acceptance rate for S: 0.6 
  Overall acceptance rate for rho: 0.22 
Finished iteration 31 


  Overall acceptance rate for S: 0.6 
  Overall acceptance rate for rho: 0.09 
Finished iteration 32 


  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.13 
Finished iteration 33 


  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.17 
Finished iteration 34 


  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.17 
Finished iteration 35 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.17 
Finished iteration 36 


  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.17 
Finished iteration 37 


  Overall acceptance rate for S: 0.66 
  Overall acceptance rate for rho: 0.17 
Finished iteration 38 


  Overall acceptance rate for S: 0.64 
  Overall acceptance rate for rho: 0.13 
Finished iteration 39 


  Overall acceptance rate for S: 0.56 
  Overall acceptance rate for rho: 0.23 
Finished iteration 40 


  Overall acceptance rate for S: 0.63 
  Overall acceptance rate for rho: 0.24 
Finished iteration 41 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.16 
Finished iteration 42 


  Overall acceptance rate for S: 0.58 
  Overall acceptance rate for rho: 0.19 
Finished iteration 43 


  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.25 
Finished iteration 44 


  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.17 
Finished iteration 45 


  Overall acceptance rate for S: 0.65 
  Overall acceptance rate for rho: 0.09 
Finished iteration 46 


  Overall acceptance rate for S: 0.57 
  Overall acceptance rate for rho: 0.13 
Finished iteration 47 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.17 
Finished iteration 48 


  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.12 
Finished iteration 49 


  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.22 
Finished iteration 50 


  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.64 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.57 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.58 
  Overall acceptance rate for rho: 0.18 
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  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.58 
  Overall acceptance rate for rho: 0.18 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.26 
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  Overall acceptance rate for rho: 0.21 
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  Overall acceptance rate for S: 0.64 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.57 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.63 
  Overall acceptance rate for rho: 0.22 
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  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.64 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.6 
  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.2 
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  Overall acceptance rate for S: 0.64 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.65 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.64 
  Overall acceptance rate for rho: 0.13 
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  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.13 
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  Overall acceptance rate for rho: 0.13 
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  Overall acceptance rate for S: 0.58 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.13 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.57 
  Overall acceptance rate for rho: 0.22 
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  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.56 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.6 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.61 
  Overall acceptance rate for rho: 0.26 
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  Overall acceptance rate for S: 0.58 
  Overall acceptance rate for rho: 0.22 
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  Overall acceptance rate for S: 0.62 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for S: 0.57 
  Overall acceptance rate for rho: 0.13 
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  Overall acceptance rate for S: 0.59 
  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.2 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.13 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.13 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.04 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.09 
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  Overall acceptance rate for rho: 0.22 
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  Overall acceptance rate for rho: 0.17 
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  Overall acceptance rate for rho: 0.2 
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  Overall acceptance rate for S: 0.64 
  Overall acceptance rate for rho: 0.17 
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DisHet documentation built on May 2, 2019, 2:42 a.m.