wrap_and_go: Main function for running GO analysis in parallel.

In vitalinakomashko/parallelGO: Parallel Implementation for Extraction of GO Results

Description

wrap_and_go serves as a wrapper function for reading the file with gene identifiers and set labels, applying minor cleaning, mapping to ENTREZ gene identifiers and calculating GO enrichment analysis in parallel.

Usage

wrap_and_go(path, col_names, delim, id, species, min_set_size, cores,
  run_parallel = TRUE, ontologies)

Arguments

path	Character string specifying the path to file. This parameter is mandatory. For the file to be processed correctly ensure that gene identifiers are in the first column and the gene set labels are in the second column of the file.
col_names	A logical value indicating presence of column names in the first line of the file. This parameter is mandatory.
delim	Character string indicating field separator character in the file. This parameter is mandatory.
id	A character string specifying the type of gene identifier in the data, must of be one of two "symbol" (default) or "ensembl". This parameter is mandatory.
species	A character string specifying the species, must be one of two "human" (default) or "mouse". This parameter is mandatory.
min_set_size	Positive integer that defines a minimum number of genes in a set. This parameter is optional. If provided all sets that don't meet the membership criteria will be removed before GO enrichment analysis.
cores	Positive integer specifying number of cores to be used for parallel computation. This parameter is optional.
run_parallel	Boolean indicating whether to run the execution in parallel. Default is TRUE. If FALSE parameter cores will be ignored.
ontologies	Optional character vector with ontologies. Valid values: CC, BP, MF. If not provided GO enrichment will be run for all categories.

Value

Data frame with the results of GO enrichment analysis.

Examples

## Not run: 
# Example 1: provide all possible parameters

 out <- wrap_and_go("path_to_my_file", col_names = TRUE, delim = ",",
 id = "symbol", species = "human", min_set_size = 30, cores = 4)

# Example 2: provide minimum necessary set of parameters (no sets will be
removed, number of cores will be determined by foreach::getDoParWorkers)

out <- wrap_and_go("path_to_my_file", col_names = TRUE, delim = ",",
id = "symbol", species = "human")

# Example 3: with ensembl gene ids instead of gene symbols:

out <- wrap_and_go("path_to_my_file", col_names = TRUE, delim = ",",
id = "ensembl", species = "human")


## End(Not run)

vitalinakomashko/parallelGO documentation built on May 18, 2019, 1:32 p.m.