IncorporateDepmap: Incorporate Depmap screen into analysis

In WubingZhang/MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Incorporate Depmap screen into analysis

Description

Incorporate Depmap screen into analysis

Usage

IncorporateDepmap(
  dd,
  symbol = "id",
  cell_lines = NA,
  lineages = "All",
  na.rm = FALSE
)

Arguments

dd	A data frame.
symbol	A character, specifying the column name of gene symbols in the data frame.
cell_lines	A character vector, specifying the cell lines for incorporation.
lineages	A character vector, specifying the cancer types for incorporation.
na.rm	Boolean, indicating whether removing NAs from the results.

Value

A data frame with Depmap column (average CERES scores across selected cell lines) attached.

Author(s)

Wubing Zhang

Examples

file1 = file.path(system.file("extdata", package = "MAGeCKFlute"),
"testdata/rra.gene_summary.txt")
gdata = ReadRRA(file1)
head(gdata)
## Not run: 
  gdata = IncorporateDepmap(gdata)
  head(gdata)

## End(Not run)

WubingZhang/MAGeCKFlute documentation built on Jan. 27, 2024, 2:43 p.m.