gdcSurvivalAnalysis {GDCRNATools} | R Documentation

## Univariate survival analysis of multiple genes

### 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)

[Package GDCRNATools version 1.4.1 Index]