romic (version 1.1.3)

filter_tomic: Filter T* Omics

Description

Filter a tidy or triple omic to entries of interest.

Usage

filter_tomic(
  tomic,
  filter_type,
  filter_table,
  filter_value,
  filter_variable = NULL
)

Value

A tomic object where a subset of features, samples or measurmenets have been filtered.

Arguments

tomic

Either a tidy_omic or triple_omic object

filter_type

category

filter filter_variable to categories specified in filter_value

range

filter filter_variable to using the range (i.e., lower and upper limit) provided in filter_value

apply

a quosure as a filter_value to a table of interest

filter_table

table where the filter should be applied

filter_value

values to filter based on

filter_variable

variable to apply the filter to

Examples

filter_tomic(
  brauer_2008_triple,
  filter_type = "category",
  filter_table = "features",
  filter_variable = "BP",
  filter_value = c("biological process unknown", "vacuolar acidification")
)

filter_tomic(
  brauer_2008_triple,
  filter_type = "category",
  filter_table = "samples",
  filter_variable = "DR",
  filter_value = 0.05
)

filter_tomic(
  brauer_2008_tidy,
  filter_type = "range",
  filter_table = "samples",
  filter_variable = "DR",
  filter_value = c(0, 0.2)
)

filter_tomic(
  brauer_2008_triple,
  filter_type = "quo",
  filter_table = "features",
  filter_value = rlang::quo(BP == "biological process unknown")
)