StromaExp function

Stroma (Immune) Component Gene Expression Estimation

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.

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)