quevedor2/CCLid: Compares Cancer Cell Line Genotypes Against Pharmacogenomic Datasets

This package has 3 main functions that all centre on analyzing the genotypes of cancer cell lines and compares them against 1,497 unique cancer cell lines analyzed across 3 large pharmacogenomic datasets. The 3 functions are to 1) identify an input cell line VCF using the genotype and B-allele fraction (BAF) as the input for a logistic regression, 2) identify regions of the genome that are drifted by scanning for segments where the BAF are significantly different from a comparator cell line, and 3) run a deconvolution on the cell line BAFs using NMF to identify if two or more cell lines are mixed and to what proportion they are.

Getting started

Package details

LicenseMIT + file LICENSE
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
quevedor2/CCLid documentation built on July 15, 2020, 4:05 a.m.