VALORATE: fast and accurate log-rank test in balanced and unbalanced comparisons of survival curves and cancer genomics

Abstract

Summary: The association of genomic alterations to outcomes in cancer is affected by a problem of unbalanced groups generated by the low frequency of alterations. For this, an R package (VALORATE) that estimates the null distribution and the P -value of the log-rank based on a recent reformulation is presented. For a given number of alterations that define the size of survival groups, the log-rank density is estimated by a weighted sum of conditional distributions depending on a co-occurrence term of mutations and events. The estimations are accurately accelerated by sampling across co-occurrences allowing the analysis of large genomic datasets in few minutes. In conclusion, the proposed VALORATE R package is a valuable tool for survival analysis.

Availability and implementation: The R package is available in CRAN at https://cran.r-project.org and in http://bioinformatica.mty.itesm.mx/valorateR .

Contact: vtrevino@itesm.mx.

Supplementary information: Supplementary data are available at Bioinformatics online.