diffxpy.api.enrich.RefSets¶
- class diffxpy.api.enrich.RefSets(sets=None, fn=None, type='gmt')¶
Class for a list of gene sets.
Input: 1. Read gene sets from file. 2. Give a list with gene sets. 3. Manually add gene sets one by one.
.gmt files can be downloaded from http://software.broadinstitute.org/gsea/msigdb/collections.jsp for example.
- __init__(sets=None, fn=None, type='gmt')¶
Methods
__init__
([sets, fn, type])add
(id, source, gene_ids)Add a gene set manually.
clean
(ids)Only keep gene ids that are contained within a full reference set of ids.
get_set
(id)Return the set with a given set identifier.
grepv_sets
(x)Search gene set identifiers for a substring.
load_sets
(sets[, type])Load gene sets from python list.
overlap
(enq_set[, set_id])Count number of overlapping genes between an internal sets and a reference set.
read_from_file
(fn[, type])Process gene sets from file.
subset
(idx)Subset RefSets object.
subset_bykey
(keys)Only keep sets that are contain at least one of a list of key strings in their identifier.