gdcKMPlot {GDCRNATools} | R Documentation

## Kaplan Meier plot

### Description

Plot Kaplan Meier survival curve

### Usage

    gdcKMPlot(gene, rna.expr, metadata, sep = "median")

### Arguments

`gene` | an Ensembl gene id
`rna.expr` | `voom` transformed expression data
`metadata` | metadata parsed from `gdcParseMetadata`
`sep` | a character string specifying which point should be used to separate low-expression and high-expression groups. Possible values are `'1stQu'`, `'mean'`, `'median'`, and `'3rdQu'`. Default is `'median'`

### Value

A plot of Kaplan Meier survival curve

### Author(s)

Ruidong Li and Han Qu

### Examples

    ####### KM plots #######
    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
    gdcKMPlot(gene='ENSG00000000938', rna.expr=rnaExpr,
        metadata=metaMatrix, sep='median')

[Package GDCRNATools version 1.7.0 Index]