Survival analyses of TCGA patients with expression in their tumors by Cox-PH method

This function makes regression models between the gene expression within tumor samples and patient overall survival time.

.plot_CoxPH_RNAseq_TCGA(gene_list, tumor)

Arguments

gene_list

gene names in a vector of characters

tumor

all tumor types or specific type

Details

This function

• selects RNAseq of the query gene, survival data and cancer types from the dataset TCGA_RNAseq_OS_sampletype prepared from initialize_survival_data().

• makes univariable regression models with .univariable_analysis() and multivariable regression models with .multivariable_analysis().

• plots the results as a forest graph with .forest_graph()

This function is not accessible to the user and will not show at the users' workspace. It can only be called by the exported EIF4F_Survival_analysis() function.

Side effects:

(1) forest graphs on screen and as pdf file to show the relation between survival of TCGA patients and expression of gene_list in their tumors by univariable and multivariable regression models

See also

Other composite function to call survival analysis and plotting: .plot_KM_RNAseq_TCGA()

Examples

if (FALSE) {
.plot_CoxPH_RNAseq_TCGA(c(
  "EIF4E", "EIF4E2", "EIF4E3",
  "EIF4G1", "EIF4G2", "EIF4G3", "EIF4A1", "EIF4A2", "EIF3D", "EIF3E",
  "EIF4EBP1", "EIF4EBP2", "MKNK1", "MKNK2", "EIF4B", "EIF4H", "MTOR", "MYC"
), "All")
}