cell_lines_filter: Filter cell-lines based on criteria

In jimvine/rcellosaurus: Cellosaurus for R

Description

An XML nodeset of cell-line elements can be filtered to produce a subset containing only those elements that match the filter criteria.

Usage

cell_lines_filter(cell_lines, filter_by, filter_term,
  filter_type = c("equals", "contains", "starts-with"))

Arguments

cell_lines	An XML nodeset containing cell-line elements. Typically either all the cell-lines in the Cellosaurus dataset, obtained using cell_lines_all, or an existing subset returned by a previous filtering.
filter_by	A string specifying which characteristic the filter should be applied to. Valid options are listed in Details.
filter_term	A string or character vector specifying the term(s) to filter on. If multiple values are provided, the filter will be applied as an "OR", i.e., retaining cell-lines that match any of the items in filter_term. The terms are case-sensitive.
filter_type	Options are c("equals", "contains","starts-with").

Details

The following options are available as filter_by terms:

• accession

• accession-primary (as accession, but only matching primary accession codes),

• accession-secondary (as accession, but only matching secondary accession codes),

• name

• name-identifier (as name, but only matching identifier (i.e., primary) names),

• name-synonym (as name, but only matching synonym (i.e., secondary) names),

• category

• sex

• species

• species-accession

• comment

• comment-category

• same-origin-as (Names of cell-lines that this cell-line has the same origin as),

• same-origin-as-accession (Accession codes of cell-lines that this cell-line has the same origin as),

• derived-from (Name of a cell-line that this cell-line is derived from),

• derived-from-accession (Accession code of a cell-line that this cell-line is derived from),

• disease (Disease by name),

• disease-accession (Disease by accession code).

For full details of the meanings of these values, see the Cellosaurus documentation.

Because filter_terms are applied to retain cell-line elements that match any of the terms (effectively a logical OR), filtering to find cell lines that match two (or more) criteria is achieved using two (or more) calls to this function.

Value

An XML nodeset containing the subset of the cell-lines that match the filter criteria. If no cell-lines match, an empty nodeset will be returned. If one cell-line matches, a nodeset with a single node will be returned.

Examples

# Set up the data
cellosaurus <- read_cellosaurus_xml(system.file("extdata",
                                                "cellosaurus.xml",
                                                package = "rcellosaurus"))
cell_lines <- cell_lines_all(cellosaurus)

# Filter for a particular accession number:
cell_lines_filter(cell_lines,
                  filter_by = "accession",
                  filter_term = "CVCL_E525",
                  filter_type = "equals")

# Filter for all cell-lines matching any of three sex categories:
cell_lines_filter(cell_lines,
                  filter_by = "sex",
                  filter_term = c("Mixed sex",
                                  "Sex ambiguous",
                                  "Sex undetermined"),
                  filter_type = "equals")

# Sequential filtering to match "disease contains dysplasia" AND
# "category contains stem cell":
dysplasia_lines <- cell_lines_filter(cell_lines,
                                     filter_by = "disease",
                                     filter_term = "dysplasia",
                                     filter_type = "contains")
dysplasia_stem_lines <- cell_lines_filter(dysplasia_lines,
                                          filter_by = "category",
                                          filter_term = "stem cell",
                                          filter_type = "contains")

jimvine/rcellosaurus documentation built on May 14, 2019, 8:04 a.m.