expressions: expressions

Description Usage Arguments Value Author(s) References Examples

View source: R/expressions.R

Description

'expressions' compares the gene expression between cancer cell lines with highest and lowest dependencies of a gene set (signature).

Usage

1
2
3
4
5
6
7
8
expressions(
  signature.name,
  signature,
  cutoff.freq = 10,
  cutoff.percentile = 0.2,
  cutoff.qvalue = 0.1,
  cutoff.fc = 2
)

Arguments

signature.name

Names of a signature (format: character)

signature

Gene names of a signature (format: vector)

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.qvalue

Cutoff for q-value of the T-test results, default 0.1

cutoff.fc

Cutoff for fold changes of the T-test results, default 2

Value

plot

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

1
2
3
4
source(system.file("script", "load_libs.R", package = "deplink"))
signature.name = "9-1-1"
signature = c("RAD9A", "RAD1", "HUS1", "RAD17")
expressions(signature.name, signature)

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