par_multiple_sets_annot: Functional annotation for multiple gene sets. Parallel...
In DanWiebe/fsgor: Package for Fold-specific GO Terms Recognition

Description Usage Arguments Value Examples

Conducts functional annotation using Fisher exact test for multiple gene sets, returns list with resulting annotations

1 2	par_multiple_sets_annot(gene_sets, annot_data, threads, gene_amount_border = 1, background_genes = NULL, p_adjust_method = "BH")

`gene_sets`	list contains quantile names (e.g. "1","2","1-6") as keys and corresponding gene sets as values
`annot_data`	list object contains annotation data ready for functional annnotation procedure, ontology relation data, GO terms full names, GO terms namespaces and metadata for annotation
`threads`	number of threads
`gene_amount_border`	minimal number of genes annotated to a term (1 by default)
`background_genes`	vector contains background set of genes
`p_adjust_method`	method for multiple testing correction (to see all possible methods print: p.adjust.methods) Benjamini-Hochberg by default

list with filenames as keys and annotaton data frames as values

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    data(up_genes, annot_data, package = "fsgor")
    gene_sets <- div_genes_to_quantiles(up_genes, 6)
    par_multiple_sets_annot(gene_sets, annot_data, threads = 6,  gene_amount_border = 10)