overlap_info {KEGGlincs} | R Documentation

## Get overlap information for pairs of gene knock-outs from 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)

[Package KEGGlincs version 1.20.0 Index]