as_annotation_list: Convert a data frame to a list of gene sets
In fosterlab/CFTK: The Co-Fractionation Toolkit

Description Usage Arguments Value Examples

Convert a data frame with gene sets and gene names in separate columns into a list of gene sets, in which the names of the list are the gene sets and the entries are vectors of genes.

1	as_annotation_list(annotations, set_col, gene_col)

`annotations`	a data frame containing some annotations
`set_col`	the name of the column that contains the gene sets (e.g. Gene Ontology terms)
`gene_col`	the name of the column that contains the annotated targets (e.g. UniProt accessions)

a named list where the names are found in keyCol and the entries are unique items from termCol

# set up a gene set data frame
ann_df = data.frame(pathway = c('a', 'a', 'a', 'b', 'c'),
                    gene = c('gene_1', 'gene_2', 'gene_3', 'gene_1', 
                             'gene_3'))
ann = as_annotation_list(ann_df, 'pathway', 'gene')
str(ann)

# go = read_gpa("goa_human.gpa.gz")
# ann = as_annotation_list(go, "GO ID", "DB Object ID")