Survival analyses of TCGA patients with expression in their tumors by Kaplan Meier method

Source: R/Survival.R

This function generates a Kaplan Meier plot to compare the expression of one gene in TCGA cancer types.

.plot_KM_RNAseq_TCGA(gene_name, cutoff, tumor)

Arguments

gene_name

gene name

cutoff

percentage of gene expression for patient stratification

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().

  • compares the survival data from patients with top or bottom percents of gene expression, and plot the results as a KM curve plot by .KM_curve().

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) KM curve plots on screen and as pdf files to correlate patient survival probability with expression of gene_name in their tumors

See also

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

Examples

if (FALSE) {
plot.km.EIF.tumor(gene_name = "EIF4E", cutoff = 0.2,
tumor = "lung adenocarcinoma")
}