goatools.rpt.goea_nt_xfrm module

Manage GOATOOLS GOEA namedtuples.

goatools.rpt.goea_nt_xfrm.get_study_items(goea_results)[source]

Get all study items found in a GOATOOLS GOEA (e.g., geneids).

goatools.rpt.goea_nt_xfrm.get_goea_nts_prt(goea_results, **kws)[source]

Get namedtuples containing user-specified (or default) data from GOATOOLS GOEA results.

class goatools.rpt.goea_nt_xfrm.MgrNtGOEAs(goea_results)[source]

Bases: object

Manage GOATOOLS GOEA namedtuples.

get_study_items()[source]

Get all study items (e.g., geneids).

get_nts_strpval(fmt='{:8.2e}')[source]

Given GOEA namedtuples, return nts w/P-value in string format.

static dflt_sortby_objgoea(goea_res)[source]

Default sorting of GOEA results.

static dflt_sortby_ntgoea(ntgoea)[source]

Default sorting of GOEA results stored in namedtuples.

get_goea_nts_prt(fldnames=None, **usr_kws)[source]

Return list of namedtuples removing fields which are redundant or verbose.

get_goea_nts_all(fldnames=None, **kws)[source]

Get namedtuples containing user-specified (or default) data from GOEA results.

Reformats data from GOEnrichmentRecord objects into lists of namedtuples so the generic table writers may be used.