annots_to_geneGO: Convert annotation table to gene or annotation list for topGO
In surh/HMVAR: Human Microbiome Variant Analysis in R

Description Usage Arguments Value Examples

Takes a data frame or tibble that maps genes to annotations, and creates either a list of genes or a list of annotation terms that can be ussed with annFUN.gene2GO or annFUN.GO2genes.

1	annots_to_geneGO(annots, direction = "geneID2GO")

`annots`	A tibble or data frame that has columns 'gene_id' and 'annots'. Column 'annots' must be a comma-separated charachter string with all the terms that annotate a given 'gene_id'.
`direction`	Either "geneID2GO" or "GO2geneID". Direction of the list that is produced.

A named list. If 'direction = "geneID2GO"', then the list has one element per 'gene_id' (named after that gene), and each element of the list is a character vector with all the terms that annotate that gene. If 'direction = "GO2geneID"', the the list has one element per annotation term in 'annots' (named after that term), and each element of the list is a character vector with all the genes annotated with that term.

d <- tibble::tibble(gene_id = c('gene1', 'gene2', 'gene3'),
                    terms = c(NA, 'term1,term2', 'term2, term3'))
annots_to_geneGO(d, direction = "geneID2GO")
annots_to_geneGO(d, direction = "GO2geneID")