KL_compare {KEGGlincs} | R Documentation

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

### 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)

[Package KEGGlincs version 1.12.0 Index]