ResembleDepmap: Compute the similarity between customized CRISPR screen with...

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

Compute the similarity between customized CRISPR screen with Depmap screens

Description

Compute the similarity between customized CRISPR screen with Depmap screens

Usage

ResembleDepmap(
  dd,
  symbol = "id",
  score = "Score",
  lineages = "All",
  method = c("pearson", "spearman", "kendall")[1]
)

Arguments

dd	A data frame.
symbol	A character, specifying the column name of gene symbols in the data frame.
score	A character, specifying the column name of gene essentiality score in the data frame.
lineages	A character vector, specifying the lineages used for common essential gene selection.
method	A character, indicating which correlation coefficient is to be used for the test. One of "pearson", "kendall", or "spearman".

Value

A data frame with correlation and test p.value.

Author(s)

Wubing Zhang

Examples

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

## End(Not run)

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