TCGAbiolinks (version 1.2.5)

TCGAanalyze_SurvivalKM: survival analysis (SA) univariate with Kaplan-Meier (KM) method.

Description

TCGAanalyze_SurvivalKM perform an univariate Kaplan-Meier (KM) survival analysis (SA). It performed Kaplan-Meier survival univariate using complte follow up with all days taking one gene a time from Genelist of gene symbols. For each gene according its level of mean expression in cancer samples, defining two thresholds for quantile expression of that gene in all samples (default ThreshTop=0.67,ThreshDown=0.33) it is possible to define a threshold of intensity of gene expression to divide the samples in 3 groups (High, intermediate, low). TCGAanalyze_SurvivalKM performs SA between High and low groups using following functions from survival package

1. survival::Surv
2. survival::survdiff
3. survival::survfit

Usage

TCGAanalyze_SurvivalKM(clinical_patient, dataGE, Genelist, Survresult, ThreshTop = 0.67, ThreshDown = 0.33, p.cut = 0.05)

Arguments

clinical_patient

is a data.frame using function 'clinic' with information related to barcode / samples such as bcr_patient_barcode, days_to_death , days_to_last_followup , vital_status, etc

dataGE

is a matrix of Gene expression (genes in rows, samples in cols) from TCGAprepare

Genelist

is a list of gene symbols where perform survival KM.

Survresult

is a parameter (default = FALSE) if is TRUE will show KM plot and results.

ThreshTop

is a quantile threshold to identify samples with high expression of a gene

ThreshDown

is a quantile threshold to identify samples with low expression of a gene

p.cut

p.values threshold. Default: 0.05

Value

table with survival genes pvalues from KM.

Examples

query <- TCGAquery(tumor = "lgg")
## Not run: 
# clinical_patient_Cancer <- TCGAquery_clinic("brca","clinical_patient")
# dataBRCAcomplete <- log2(BRCA_rnaseqv2)
# # Selecting only 10 genes for example
# dataBRCAcomplete <- dataBRCAcomplete[1:10,]
# tabSurvKM<-TCGAanalyze_SurvivalKM(clinical_patient_Cancer,dataBRCAcomplete,
# Genelist = rownames(dataBRCAcomplete), Survresult = FALSE,ThreshTop=0.67,ThreshDown=0.33)
# ## End(Not run)