In DrugComb/TidyComb: Preparing drug combination data for DrugComb

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(TidyComb)

TidyComb uses information from ExpasyCellosaurus to generate cell line annotations. As Cellosaurus doesn't provide API, TidyComb embeded whole Cellosaurus data from Cellosaurus in the package.

1. Check Cellosaurus database version

By defaut, function CellVersion() will check the current online Cellosaurus data version

CellVersion()

Version of the Cellosaurus data embedded by TidyComb can be shown wih:

CellVersion(file = system.file("cellosaurus.xml", package = "TidyComb"))

Note: If you find the embedded Cellosaurus data is too old. You can download newest data from ftp://ftp.expasy.org/databases/cellosaurus and save it in your work directory and use this file in the following functions.

2. Get cellosaurus accession with cell line name

Cellosaurus accession is the unique identifier used by Cellosaurus to archive cell lines

cell_name <- c("U87", "HSTS", "LNCAP")
MatchCellAcc(cell_name, file = system.file("cellosaurus.xml", package = "TidyComb")) # I'm using the embedded data. You can change is into the file downloaded by yourself

3. Get cell line information with cellosaurus accession

doc <- ParseCell(file = system.file("cellosaurus.xml", package = "TidyComb")) # I'm using the embedded data. You can change is into the file downloaded by yourself
GetCellInfo(c("CVCL_0022", "CVCL_0395"), doc)