OmitCommonEssential: Omit common essential genes based on depmap data

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

Omit common essential genes based on depmap data

Description

Omit common essential genes based on depmap data

Usage

OmitCommonEssential(
  dd,
  symbol = "id",
  lineages = "All",
  cell_lines = NULL,
  dependency = -0.5
)

Arguments

dd	A data frame.
symbol	A character, specifying the column name of gene symbols in the data frame.
lineages	A character vector, specifying the lineages for selecting essential genes.
cell_lines	A character vector, specifying cell lines for selecting essential genes.
dependency	A numeric, specifying the threshold for selecting essential genes.

Value

A data frame.

Author(s)

Wubing Zhang

Examples

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

## End(Not run)

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