path_genes_by_cell_type: See how many pathway gene knock-outs are available from data

In KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data

Description

Check quantity of data across cell lines available from LINCS corresponding to the pathway of interest

Usage

path_genes_by_cell_type(KEGG_mappings, pert_time = 96, get_KOs = FALSE,
  generate_plot = TRUE)

Arguments

KEGG_mappings	KEGG_mappings The data.frame object generated by the function expand_KEGG_mappings
pert_time	Choose from (6,24,48,96,120,144,168)
get_KOs	Logical indicator to have data frame returned
generate_plot	Logical indicator to generate histogram

Value

A plot depicting percentage of pathway genes knocked-out by cell line and a data frame object listing the genes [by cell line]

Examples

p53_KGML <- get_KGML("hsa04115")
p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML)

path_genes_by_cell_type(p53_KEGG_mappings)

KEGGlincs documentation built on Nov. 8, 2020, 5:47 p.m.