| gdcSurvivalAnalysis {GDCRNATools} | R Documentation |
Univariate Cox Proportional-Hazards and Kaplan Meier survival analysis of a vector of genes
gdcSurvivalAnalysis(gene, rna.expr, metadata, method = "coxph", sep = "median")
gene |
a vector of Ensembl gene ids |
rna.expr |
|
metadata |
metadata parsed from |
method |
method for survival analysis. Possible values are
|
sep |
which point should be used to separate low-expression
and high-expression groups for |
A dataframe or numeric matrix of hazard ratio, 95% confidence interval, p value, and FDR
Ruidong Li and Han Qu
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.
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)