KL_compare: Combines all other package functions for one-step cell line...

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

Description

Combines all other package functions for one-step cell line comparison

Usage

KL_compare(pathwayid, cell_line1 = NA, cell_line2 = NA,
  refine_by_cell_line = TRUE, data_type = "100_full", pert_time = 96,
  only_mapped = TRUE, get_data = FALSE, convert_KEGG_IDs = TRUE,
  graph_title = "default", tidy_edge = TRUE, layered_nodes = FALSE)

Arguments

pathwayid	A KEGG pathway ID of the form "hsa12345" (only human pathways currently)
cell_line1	Choose from the set of cell lines: (A375,A549,ASC,HA1E,HCC515,HEK293T,HEKTE,HEPG2,HT29,MCF7,NCIH716,NPC,PC3, SHSY5Y,SKL,SW480,VCAP)
cell_line2	A cell line such that cell_line1 != cell_line2
refine_by_cell_line	A logical indicator
data_type	Choose from data types: (100_full, 100_bing, 50_lm)
pert_time	Choose from (6,24,48,96,120,144,168)
only_mapped	A logical indicator; if set to FALSE will return 'de-novo' edges that 'exist' in data but are not documented in KEGG
get_data	A logical indicator; if set to true, will return the 'expanded' edge information for the specified pathway
convert_KEGG_IDs	A logical indicator; if set to TRUE KEGG compounds will remain labeled via KEGG codes (do not need KEGGREST)
graph_title	An optional user-specified graph title
tidy_edge	A logical indicator; must be set to FALSE for expanded edges
layered_nodes	A logical indicator; if set to TRUE will create a graph with 'stacked' nodes that the user can manipulate when multiple nodes are mapped to one location

Value

A dynamic map in Cytoscape automatically formatted for convenient viewing and, if idicated by user, a data.frame object with detailed information for 'expanded' KEGG edges

Examples

## Not run:  

# Compare p53 pathway between cell lines A375 and A549:
KL_compare("hsa04115", "A375", "A549")

## End(Not run)

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