depmap_annotate: annotate essential genes w/DepMap

Description Usage Arguments Value Examples

View source: R/depmap_annotate.R

Description

Takes a vector of depmap genes, and annotates the genes as esseintail or not essential given a cutoff. For details and downloads please visit https://depmap.org/portal/

Usage

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depmap_annotate(cnr, depMeans, cutoff = -0.5)

Arguments

cnr

a cnr bundle

depMeans

an object with the dependency score means for the cells of interest

cutoff

cutoff of D2 score to consider essential gene or non-essentail gene

Value

Function returns the gene.index with depmap annotation colums; both depMeans, and essential (essentian/non-essential)

Examples

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## Not run: 
d2_map <- read.csv("inst/extdata/D2_combined_gene_dep_scores.csv.gz",
 header = TRUE, row.names = 1)

## select cells to use
keep <- grep("BONE", names(depmap))

d2_bone <- DepScores(depmap = d2_map, keep = keep)

depMeans <- rowMeans(d2_bone[,keep])

depmap_annotate(cnr, depMeans = depMeans)


## End(Not run)

SingerLab/gac documentation built on July 22, 2021, 3:27 a.m.