dot-prepare_variables_topoicsim: GAPGOM internal - .prepare_variables_topoicsim()

Description Usage Arguments Details Value Notes

Description

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

Usage

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.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).


Berghopper/GAPGOM documentation built on July 2, 2020, 11:57 p.m.