In vjcitn/ccleR6: ccleR6

BiocStyle::markdown()

Sys.setenv("CCLEDB_PATH"="/Users/stvjc/Research/CCLE_CHAPMAN/CellLineData.db")
suppressPackageStartupMessages({
library(ccleR6)
})

Introduction

A large indexed SQLite database has been created by Phil Chapman to represent CCLE, Achilles, and other integrative data sources relevant to cancer biology.

This document describes some approaches to user interface design. We indicate how to

• query the database directly
• provide R-level support for substantively useful self-description
• carry out some exemplary 'analyses'

For this code to work you need to have the environment variable CCLEDB_PATH defined to give the path to the SQLite file.

An R6 interface

I believe that an object that is somewhat fleshed out relative to the database view provided by dplyr will come in handy. Therefore I defined a reference class and have lightly populated it with some identifier vectors.

ccle = ccledb$new(.ccleSrc)
ccle
"BRAF" %in% ccle$cngenes  # copy number gene list

I have not done much with this yet but I think this will help with subsetting and shiny query support.

dplyr-based interaction

We can get a feel for the contents with some simple commands. .ccleSrc is a globally defined dplyr src.

library(ccleR6)
.ccleSrc
.ccleSrc %>% tbl("ccle_cell_line_info") %>% head()

Gene annotation

Expression data are provided at probe-set level, with symbols.

.ccleSrc %>% tbl("ccle_exprs_tall") %>% head()

Compound annotation

.ccleSrc %>% tbl("ccle_drug_data") %>% head()

vjcitn/ccleR6 documentation built on May 3, 2019, 6:14 p.m.