BiocStyle::markdown()
Sys.setenv("CCLEDB_PATH"="/Users/stvjc/Research/CCLE_CHAPMAN/CellLineData.db") suppressPackageStartupMessages({ library(ccleR6) })
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
For this code to work you need to have the environment variable
CCLEDB_PATH
defined to give the path to the SQLite file.
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.
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()
Expression data are provided at probe-set level, with symbols.
.ccleSrc %>% tbl("ccle_exprs_tall") %>% head()
.ccleSrc %>% tbl("ccle_drug_data") %>% head()
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