overlap_info: Get overlap information for pairs of gene knock-outs from...

In shanawhite-UC/KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data

Description

Get overlap information for pairs of gene knock-outs from LINCS data

Usage

overlap_info(KGML_file, KEGG_mappings, cell_type, data_type = "100_full",
  pert_time = 96, only_mapped = TRUE, affy_based = FALSE,
  keep_counts_only = TRUE, add_fisher_information = TRUE,
  p.adjust.method = "BH")

Arguments

KGML_file	An object of formal class KEGGPathway
KEGG_mappings	The data.frame object generated by the function expand_KEGG_mappings
cell_type	Choose from the set of cell lines: (A375,A549,ASC,HA1E,HCC515,HEK293T,HEKTE,HEPG2,HT29,MCF7,NCIH716,NPC,PC3, SHSY5Y,SKL,SW480,VCAP)
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
affy_based	A logical indicator; if set to TRUE will return lists/counts based on probeID instead of gene symbol.
keep_counts_only	A logical indicator; if set to FALSE will return data frame with lists [of gene symbols or probe ids] as well as counts
add_fisher_information	A logical indicator; by default the relationships are analyzed for strength of correlation via Fisher's Exact Test
p.adjust.method	For available methods, type 'p.adjust.methods' into command promt and press enter.

Value

A data frame where each row corresponds to information for pairs of experimental gene knock-outs from LINCS data (found in selected pathway).

Examples

p53_KGML <- get_KGML("hsa04115")
p53_KEGG_mappings <-  expand_KEGG_mappings(p53_KGML)
p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)

summary <- path_genes_by_cell_type(p53_KEGG_mappings)
p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, 
                               "HA1E", data_type = "100_bing", 
                               only_mapped = FALSE)

shanawhite-UC/KEGGlincs documentation built on May 29, 2019, 8:07 p.m.