README.md

In Solatar/setR:

setR

Functions used to manage gene sets

accessing DepMap data

The package includes tables from the depmap database (https://depmap.org/portal/), namely dmExpr (mRNA abundancies), dmProt (protein abundancies), demDep (genetic dependencies found by CRISPR-ko screen) and dmDrug (drug effects). The whole process of accessing the data is broken down into 2 functions.

Step 1: filtering for the cell lines you want. The deepFilter function access meta data about the cell lines and lets you filter for all possible aspects. You can use use deepFilter() without any arguments to look at the possibilies and then decide what aspect you need to filter for. We are looking for AML (acute myeloid leukemia) cell lines, so we use the lineage_subtype filter. Note that the search is done with the grepl command, so looking for "AML" would also find "AMLX". To prevent this you can enclose your term like this: "^AML$". You can look at the cell lines you found, their names are in the "stripped_cell_line" column. The output of deepFilter is a regular data.frame, so if you want to exclude certain cell lines (i.e. rows) you can do so with the subset or filter function as usual.

t(deepFilter()[1:2,])
cells <- deepFilter(lineage_subtype = "AML")
cells$stripped_cell_line_name

Step 2: getting the data for the cell lines. The deepResult function takes the output from deepFilter and the data type of your choice. Here we choose dmDep to get the dependencies the cell lines have for genes.

result <- deepResult(cells, dmDep)
result[1:5,1:5]

Solatar/setR documentation built on Dec. 5, 2020, 10:50 p.m.