Victor Treviño1, Jose Tamez-Pena1. 1. Cátedra de Bioinformática, Escuela de Medicina, Tecnológico de Monterrey, Monterrey N.L., México.
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.
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.
Authors: Monica M Olcina; Nikolas G Balanis; Ryan K Kim; B Arman Aksoy; Julia Kodysh; Michael J Thompson; Jeff Hammerbacher; Thomas G Graeber; Amato J Giaccia Journal: Cell Rep Date: 2018-12-26 Impact factor: 9.423