Filter functions

Functions to filter objects

filter_chromosomes(grlist, keep_chr = paste0("chr", c(seq_len(22), "X", "Y")))

filter_dt(dat, filters)

filter_graph(
  g,
  node_filters = list(),
  edge_filters = list(),
  rm_isolated = TRUE,
  size = NULL
)

filter_kg(
  g,
  from_categories = paste0("biolink:", c("Disease", "PhenotypicFeature",
    "GrossAnatomicalStructure", "AnatomicalEntity", "Cell")),
  to_categories = from_categories,
  edge_categories = NULL,
  dbs = NULL,
  rm_isolated = TRUE,
  as_dt = FALSE
)

filter_ontology(
  ont,
  terms = NULL,
  remove_terms = NULL,
  keep_descendants = NULL,
  remove_descendants = NULL,
  include_self = TRUE,
  use_simona = FALSE,
  ...
)

Arguments

grlist

Named list of GRanges objects.

keep_chr

Which chromosomes to keep.

filters

A named list, where each element in the list is the name of a column in the data, and the vector within each element represents the values to include in the final data.

g

tbl_graph object.

node_filters

A named list of filters to apply to the node data. Names should be name of the metadata column, and values should be a vector of valid options. For example, list("type" = c("gene","variant")) will return any rows where the "type" column contains either "gene" or "variant".

edge_filters

A named list of filters to apply to the edge data.

ont

An ontology of class ontology_DAG.

terms

A vector of ontology term IDs.

remove_terms

Character vector of term IDs to exclude.

keep_descendants

Terms whose descendants should be kept (including themselves). Set to NULL (default) to skip this filtering step.

remove_descendants

Terms whose descendants should be removed (including themselves). Set to NULL (default) to skip this filtering step.

use_simona

Use dag_filter to filter terms.

...

Arguments passed on to simona::dag_filter

dag

An ontology_DAG object.

relations

A vector of relations. The sub-DAG will only contain these relations. Valid values of "relations" should correspond to the values set in the relations argument in the create_ontology_DAG(). If relations_DAG is already provided, offspring relation types will all be selected. Note "is_a" is always included.

root

A vector of term names which will be used as roots of the sub-DAG. Only these with their offspring terms will be kept. If there are multiple root terms, a super root will be automatically added.

leaves

A vector of leaf terms. Only these with their ancestor terms will be kept.

mcols_filter

Filtering on columns in the meta data frame.

namespace

The prefix before ":" of the term IDs.

Value

Converted data.

Named list of GRanges objects.

Functions

• filter_chromosomes(): filter_ Remove non-standard chromosomes

  Remove non-standard chromosomes from a list of GRanges objects.

• filter_dt(): filter_ Filter a data.table.

• filter_graph(): filter_ Filter a tbl_graph.

• filter_kg(): filter_

  Filter the monarch knowledge graph to only include edges between specific types of nodes (e.g. Disease <–> Cell).

• filter_ontology(): filter_ Filter ontology

  Filter ontology by terms.

Examples

dat <- mtcars 
dat2 <- filter_dt(dat, filters=list(cyl=c(4,6)))
#> Filtered 'cyl' : 14 / 32 rows dropped.
if (FALSE) { # \dontrun{
g <- get_monarch_kg()
g2 <- filter_kg(g)
} # }
ont <- get_ontology("hp")
#> Loading cached ontology: /github/home/.cache/R/KGExplorer/hp.rds
ont2 <- filter_ontology(ont,terms=c("HP:0000001","HP:0000002"))
#> Translating ontology terms to ids.
ont3 <- filter_ontology(ont,terms=100)
#> Randomly sampling 100 term(s).