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.