gdcSurvivalAnalysis: Univariate survival analysis of multiple genes

In GDCRNATools: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Description

Univariate Cox Proportional-Hazards and Kaplan Meier survival analysis of a vector of genes

Usage

gdcSurvivalAnalysis(gene, rna.expr, metadata, method = "coxph",
  sep = "median")

Arguments

gene	a vector of Ensembl gene ids
rna.expr	voom transformed expression data
metadata	metadata parsed from gdcParseMetadata
method	method for survival analysis. Possible values are 'coxph' and 'KM'. Default is 'coxph'
sep	which point should be used to separate low-expression and high-expression groups for method='KM'. Possible values are '1stQu', 'mean', 'median', and '3rdQu'. Default is 'median'

Value

A dataframe or numeric matrix of hazard ratio, 95% confidence interval, p value, and FDR

Author(s)

Ruidong Li and Han Qu

References

Therneau TM, Lumley T. Package ‘survival’.
Andersen PK, Gill RD. Cox's regression model for counting processes: a large sample study. The annals of statistics. 1982 Dec 1:1100-20.
Therneau TM, Grambsch PM. Extending the Cox model. Edited by P. Bickel, P. Diggle, S. Fienberg, K. Krickeberg. 2000:51.
Harrington DP, Fleming TR. A class of rank test procedures for censored survival data.Biometrika. 1982 Dec 1;69(3):553-66.

Examples

genes <- c('ENSG00000000938','ENSG00000000971','ENSG00000001036',
        'ENSG00000001084','ENSG00000001167','ENSG00000001460')

samples <- c('TCGA-2F-A9KO-01', 'TCGA-2F-A9KP-01',
            'TCGA-2F-A9KQ-01', 'TCGA-2F-A9KR-01',
            'TCGA-2F-A9KT-01', 'TCGA-2F-A9KW-01')
             
metaMatrix <- data.frame(sample_type=rep('PrimaryTumor',6),
                        sample=samples,
                        days_to_death=seq(100,600,100),
                        days_to_last_follow_up=rep(NA,6))
rnaExpr <- matrix(c(2.7,7.0,4.9,6.9,4.6,2.5,
                    0.5,2.5,5.7,6.5,4.9,3.8,
                    2.1,2.9,5.9,5.7,4.5,3.5,
                    2.7,5.9,4.5,5.8,5.2,3.0,
                    2.5,2.2,5.3,4.4,4.4,2.9,
                    2.4,3.8,6.2,3.8,3.8,4.2),6,6)
rownames(rnaExpr) <- genes
colnames(rnaExpr) <- samples
survOutput <- gdcSurvivalAnalysis(gene=genes,
    rna.expr=rnaExpr, metadata=metaMatrix)

GDCRNATools documentation built on Nov. 27, 2020, 2 a.m.