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

In MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic 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)

MAGeCKFlute documentation built on Nov. 8, 2020, 5:40 p.m.