rna_majiq.PsiControlsSummary

class rna_majiq.PsiControlsSummary(df, events, hold_temporary=())

Summary of PSI posterior means over large group of controls

Summary of PSI posterior means over large group of controls noting the number of experiments which passed and quantiles over the experiments which passed

Parameters:

df (xarray.Dataset) – With coordinates/variables in cls.EXPECTED_VARIABLES and attribute prefixes: List[str]
events (xarray.Dataset) – dataset that can be loaded along with matching introns/junctions as Events
hold_temporary (Sequence[TemporaryDirectory]) – Hold onto temporary directories, preventing their deletion (used by PsiControlsSummary.from_psi() for temporary store of rechunked parameters)

See also

PsiControlsSummary.from_psi, PsiControlsSummary.from_zarr

__init__(df, events, hold_temporary=())

Methods

`__init__`(df, events[, hold_temporary])
`events_to_zarr`(path, mode[, consolidated])	Save events information to specified path
`from_psi`(psi[, alpha])
`from_zarr`(path)
`get_events`(introns, junctions)	Construct `Events` using saved dataset and introns, junctions
`passed_min_experiments`([min_experiments_f])	Get boolean mask of events that pass enough experiments
`to_zarr`(path[, consolidated, show_progress])	Save PSI coverage dataset as zarr

Attributes

`EVENTS_EXPECTED_VARIABLES`
`EXPECTED_VARIABLES`
`alpha`	alias for controls_alpha
`controls_alpha`
`controls_q`
`event_size`	array(ec_idx) total number of connections from same event
`is_lb`
`lsv_idx`	array(ec_idx) index identifying event it belongs to
`lsv_offsets`	array(e_offsets_idx) offsets for events into ec_idx
`num_connections`	Total number of connections over all events
`num_events`	Total number of events
`num_passed`
`num_prefixes`
`prefixes`
`psi_median`
`psi_quantile`
`psi_range`	For each controls_alpha, range between lower/upper quantiles (scale)
`q`	alias for controls_q
`total_median`
`total_quantile`