gene_ingress: Parse gene summary data for easier plotting and display

In j-andrews7/CRISPRball: Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

Parse gene summary data for easier plotting and display

Description

Parse gene summary data for easier plotting and display

Usage

gene_ingress(
  df,
  sig.thresh,
  es.thresh,
  es.col,
  sig.col,
  positive.ctrl.genes = NULL,
  essential.genes = NULL,
  depmap.genes = NULL
)

Arguments

df	data.frame of gene summary data. Gene IDs should be in the first column.
sig.thresh	Numeric scalar for significance threshold to consider a gene a hit.
es.thresh	Numeric scalar for absolute log fold change threshold to consider a gene a hit.
es.col	Character scalar for the column name of the effect size value.
sig.col	Character scalar for the column name of the significance value.
positive.ctrl.genes	Character vector of gene identifiers to label as positive controls.
essential.genes	Character vector of gene identifiers to label as essential genes.
depmap.genes	data.frame of DepMap gene summary data.

Value

A data.frame of gene summary with additional, easier to plot, columns added.

Author(s)

Jared Andrews

Examples

library(CRISPRball)
d1.genes <- read.delim(system.file("extdata", "esc1.gene_summary.txt",
    package = "CRISPRball"
), check.names = FALSE)
out.df <- gene_ingress(d1.genes, 0.05, 0.5, es.col = "LFC", sig.col = "fdr")

j-andrews7/CRISPRball documentation built on Nov. 30, 2023, 7:34 p.m.