filter_intercell: Filter intercell annotations

In saezlab/OmnipathR: OmniPath web service client and more

Filter intercell annotations

Description

Filters a data frame retrieved by import_omnipath_intercell.

Usage

filter_intercell(
  data,
  categories = NULL,
  resources = NULL,
  parent = NULL,
  scope = NULL,
  aspect = NULL,
  source = NULL,
  transmitter = NULL,
  receiver = NULL,
  secreted = NULL,
  plasma_membrane_peripheral = NULL,
  plasma_membrane_transmembrane = NULL,
  proteins = NULL,
  causality = NULL,
  topology = NULL,
  ...
)

Arguments

data	An intercell annotation data frame as provided by import_omnipath_intercell.
categories	Character: allow only these values in the category column.
resources	Character: allow records only from these resources.
parent	Character: filter for records with these parent categories.
scope	Character: filter for records with these annotation scopes. Possible values are generic and specific.
aspect	Character: filter for records with these annotation aspects. Possible values are functional and locational.
source	Character: filter for records with these annotation sources. Possible values are composite and resource_specific.
transmitter	Logical: if TRUE only transmitters, if FALSE only non-transmitters will be selected, if NULL it has no effect.
receiver	Logical: works the same way as transmitters.
secreted	Logical: works the same way as transmitters.
plasma_membrane_peripheral	Logical: works the same way as transmitters.
plasma_membrane_transmembrane	Logical: works the same way as transmitters.
proteins	Character: filter for annotations of these proteins. Gene symbols or UniProt IDs can be used.
causality	Character: filter for records with these causal roles. Possible values are transmitter and receiver. The filter applied simultaneously to the transmitter and receiver arguments, it's just a different notation for the same thing.
topology	Character: filter for records with these localization topologies. Possible values are secreced, plasma_membrane_peripheral and plasma_membrane_transmembrane; the shorter notations sec, pmp and pmtm can be used. Has the same effect as the logical type arguments, just uses a different notation.
...	Ignored.

Value

The intercell annotation data frame filtered according to the specified conditions.

Examples

ic <- import_omnipath_intercell()
ic <- filter_intercell(
    ic,
    transmitter = TRUE,
    secreted = TRUE,
    scope = "specific"
)

saezlab/OmnipathR documentation built on April 12, 2024, 3:29 p.m.