.prepare_variables_topoicsim {GAPGOM} | R Documentation

## GAPGOM internal - .prepare_variables_topoicsim()

### Description

This function is an internal function and should not be called by the user.

### Usage

    .prepare_variables_topoicsim(organism, ontology, gene_list1 = NULL,
      gene_list2 = NULL, custom_genes1 = NULL, custom_genes2 = NULL,
      drop = NULL, verbose = FALSE, debug = FALSE, progress_bar = NULL,
      use_precalculation = TRUE, garbage_collection = NULL,
      all_go_pairs = NULL, topoargs = list(), term_only = FALSE,
      keytype = "ENTREZID", go_data = NULL)

### Arguments

`organism` | where to be scanned genes reside in, this option is neccesary to select the correct GO DAG. Options are based on the org.db bioconductor package; http://www.bioconductor.org/packages/release/BiocViews.html#___OrgDb Following options are available: "fly", "mouse", "rat", "yeast", "zebrafish", "worm", "arabidopsis", "ecolik12", "bovine", "canine", "anopheles", "ecsakai", "chicken", "chimp", "malaria", "rhesus", "pig", "xenopus".
`ontology` | desired ontology to use for similarity calculations. One of three; "BP" (Biological process), "MF" (Molecular function) or "CC" (Cellular Component).
`gene_list1` | The first gene vector of gene IDs. Note; THIS IS NOT THE ENSEMBLID. Instead use the gene ID adopted by NCBI.
`gene_list2` | Same type as gene_list1, will be compared to gene_list1.
`drop` | vector of evidences in go data structure you want to skip (see set_go_data).
`verbose` | set to true for more informative/elaborate output.
`progress_bar` | Whether to show the progress of the calculation (default = FALSE)
`garbage_collection` | whether to do R garbage collection. This is useful for very large calculations/datasets, as it might decrease ram usage. This option might however increase calculation time.
`all_go_pairs` | dataframe of GO Term pairs with a column representing similarity between the two. You can add the dataframe from previous runs to improve performance (only works if the last result has at least part of the genes of the current run). You can also use it for pre-calculation and getting the results back in a fast manner.
`topoargs` | topoargs list that needs correction, default is a brand new list
`term_only` | specify if you only want arguments/params for TERM level.
`keytype` | keytype used in querying of godata
`go_data` | prepared go_data, from the set_go_data function. It is practically the same as in GOSemSim, but with a slightly nicer interface.

### Details

Prepares a list of intermediary arguments/parameters needed by topocisim.

### Value

list with all topoicsim arguments (can differ depending on algorithm level gene/geneset/term); organism, ontology, verbose, IC (Information Content from the go_data/go consortium), weighted_dag (DAG with weighted nodes), go_annotation (GO annotation of the correct root node), root (root node of the GO tree (MF, BP or CC) in annotationdbi-database string form), drop, progress_bar, garbage_collection, all_go_pairs, selected_freq_go_pairs (precalculated common GO_pairs that might increase performance), translation_to_goids (translation dataframe between ID and GOID.)

### Notes

Internal function used in (topo_ic_sim_genes).

[Package GAPGOM version 1.4.0 Index]