deplink: deplink

In seanchen607/deplink: Compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature)

Description

'deplink' compares the genetic/epigenetic features between cancer cell lines with different dependencies of a gene set (signature).

Usage

deplink(
  signature.name,
  signature,
  outputDir = "~",
  cutoff.freq = 10,
  cutoff.percentile = 0.2,
  cutoff.pvalue = 0.05,
  cutoff.qvalue = 0.1,
  cutoff.diff = 0.1,
  cutoff.fc = 2
)

Arguments

signature.name	Names of a signature (format: character)
signature	Gene names of a signature (format: vector)
outputDir	Output directory, default root directory (format: character)
cutoff.freq	Cutoff for frequency of cancer cell lines for each cancer type, default 10
cutoff.percentile	Cutoff for percentile of cancer cell lines with highest/lowest dependency, default 0.2
cutoff.pvalue	Cutoff for p-value of the T-test results, default 0.05
cutoff.qvalue	Cutoff for q-value of the T-test results, default 0.1
cutoff.diff	Cutoff for difference of the T-test results, default 0.1
cutoff.fc	Cutoff for fold changes of the T-test results, default 2

Value

message

Author(s)

Xiao Chen

References

1. X Chen, J McGuire, F Zhu, X Xu, Y Li, D Karagiannis, R Dalla-Favera, A Ciccia, J Amengual, C Lu (2020). Harnessing genetic dependency correlation network to reveal chromatin vulnerability in cancer. In preparation.

Examples

source(system.file("script", "load_libs.R", package = "deplink"))
signature.name = "9-1-1"
signature = c("RAD9A", "RAD1", "HUS1", "RAD17")
deplink(signature.name, signature)

seanchen607/deplink documentation built on Nov. 18, 2020, 11:15 a.m.