Package 'mskcc.oncotree'

Get tumor types

Description

Get tumor types according to OncoTree's ontology.

Usage

get_tumor_types(oncotree_version = "oncotree_latest_stable")

Arguments

oncotree_version

OncoTree version. Check available options with get_versions().

Value

A tibble of 13 variables:

oncotree_version

OncoTree tumor classification system version.

oncotree_code

Tumor type code: a unique identifier for a tumor type within the classification system of the OncoTree.

oncotree_name

Tumor type name: a brief description of the tumor type.

oncotree_main_type

Tumor main type: a category under which the tumor type can be grouped.

tissue

Tissue associated with the tumor type.

level

OncoTree is a hierachical classification system with 5 levels. At the root level (level 0) there is the single "TISSUE" tumor type. At level 1, there are 32 tissue sites, e.g., "BREAST".

parent

The parent is the parent oncotree_code for this tumor type.

umls_code

The corresponding tumor type identifier(s) in the Unified Medical Language System (UMLS).

nci_code

The corresponding tumor type identifier(s) in the National Cancer Institute (NCI) Thesaurus.

history

Previous tumor type codes (from previous OncoTree versions) used to identify this tumor type.

revocations

TODO.

precursors

TODO.

color

Color associated with the tumor type.

Examples

## Not run: 
get_tumor_types()

## End(Not run)

---

Get OncoTree versions

Description

Get OncoTree versions

Usage

get_versions()

Value

A tibble of four variables:

oncotree_version

OncoTree tumor classification system version.

description

OncoTree release description.

visible

A logical indicating whether this OncoTree version is visible, i.e. a forefront option at the website.

release_date

OncoTree release date.

Examples

## Not run: 
get_versions()

## End(Not run)

---

Map tumor types across ontologies

Description

This function maps codes (identifiers) across tumor classification systems. Use the arguments from and to to choose the source and target ontologies. Available options are: 'oncotree_code', 'nci_code', 'umls_code', 'icdo_topography_code', 'icdo_morphology_code', and 'hemeonc_code'.

Note that you can also use the functions oncotree_to_nci(), nci_to_oncotree(), oncotree_to_umls() and umls_to_oncotree() to map between OncoTree and NCIt systems. The difference is that these functions use the OncoTree API, and the output can be made to depend on older versions of OncoTree. map_ontology_code() relies on a static file provided by the OncoTree team that is not as up to date as the data provided by the web API. Nevetheless, the scope of the mappings provided by map_ontology_code() is broader. The file used by map_ontology_code() can be directly imported into R using the function read_ontology_mappings().

Usage

map_ontology_code(code, from, to, collapse = NULL)

Arguments

code	A character vector with identifier codes of the from ontology that are meant to be mapped to the to ontology.
from	The source ontology. One of: 'oncotree_code', 'nci_code', 'umls_code', 'icdo_topography_code', 'icdo_morphology_code', and 'hemeonc_code'.
to	The target ontology. One of: 'oncotree_code', 'nci_code', 'umls_code', 'icdo_topography_code', 'icdo_morphology_code', and 'hemeonc_code'.
collapse	A function that expects one argument, it will be the character vector of codes in the to variable, that are to be "collapsed". When the mapping is one-to-many, passing a collapsing function will allow you to make the mapping one-to-one. See examples.

Value

A tibble of two variables: first column is corresponds to the from variable and the second is the to variable.

Source

The mappings here provided are based on the file https://github.com/cBioPortal/oncotree/blob/master/scripts/ontology_to_ontology_mapping_tool/ontology_mappings.txt.

See Also

oncotree_to_nci(), nci_to_oncotree(), oncotree_to_umls() and umls_to_oncotree().

Examples

## Not run: 
# Omit the `code` argument to get all possible mappings. Note that
# one-to-many mappings will generate more than one row per `from` code.
map_ontology_code(from = 'oncotree_code', to = 'nci_code')

# Simple example
map_ontology_code('MMB', from = 'oncotree_code', to = 'nci_code')

# Some mappings are one-to-many, e.g. "SRCCR", which means repeated rows for
# the same input code.
map_ontology_code('SRCCR', from = 'oncotree_code', to = 'nci_code')

# Using the `collapse` argument to "collapse" one-to-many mappings makes sure
# that the output has as many rows as the `from` vector.
map_ontology_code('SRCCR',
                  from = 'oncotree_code',
                  to = 'nci_code',
                  collapse = toString)

map_ontology_code('SRCCR',
                  from = 'oncotree_code',
                  to = 'nci_code',
                  collapse = list)

map_ontology_code(
  'SRCCR',
  from = 'oncotree_code',
  to = 'nci_code',
  collapse = \(x) paste(x, collapse = ' ')
)

# `map_ontology_code()` is vectorized over `code`
map_ontology_code(
  c('AASTR', 'MDEP'),
  from = 'oncotree_code',
  to = 'nci_code'
  )

# Map from ICDO topography to ICDO morphology codes
map_ontology_code(
  'C72.9',
  from = 'icdo_topography_code',
  to = 'icdo_morphology_code'
  )

## End(Not run)

---

Map NCI to OncoTree codes

Description

This function maps National Cancer Institute Thesaurus (NCIt) codes to OncoTree codes.

Usage

nci_to_oncotree(
  nci_code = NULL,
  oncotree_version = "oncotree_latest_stable",
  expand = FALSE
)

Arguments

nci_code	NCI codes.
oncotree_version	OncoTree database release version.
expand	Whether to expand one-to-many mappings. If TRUE, one-to-many mappings are expanded into several rows in the output.

Value

A tibble of two variables: nci_code and oncotree_code.

Examples

## Not run: 
# Leave `nci_code` empty to return mappings for all NCI codes
nci_to_oncotree()

# Map a few selected OncoTree codes
nci_to_oncotree(nci_code = c('C8969', 'C4862', 'C9168', 'C7967'))

# Use `expand` to make sure the column `oncotree_code` is a character vector
# and not a list-column. One-to-many mappings will result in more than row
# with `oncotree_code` values repeated.
nci_to_oncotree(nci_code = c('C8969', 'C4862', 'C9168', 'C7967'), expand =
TRUE)

## End(Not run)

---

Map OncoTree to NCIt codes

Description

This function maps OncoTree codes to National Cancer Institute Thesaurus (NCIt) codes.

Usage

oncotree_to_nci(
  oncotree_code = NULL,
  oncotree_version = "oncotree_latest_stable",
  expand = FALSE,
  keep_empty = TRUE
)

Arguments

oncotree_code	OncoTree codes.
oncotree_version	OncoTree database release version.
expand	Whether to expand one-to-many mappings. If TRUE, one-to-many mappings are expanded into several rows in the output.
keep_empty	OncoTree codes that do not map to NCI have the nci_code with NA if keep_empty = TRUE. Use keep_empty = FALSE, to remove the mapping (row) altogether from the output.

Value

A tibble of two variables: oncotree_code and nci_code.

Examples

## Not run: 
# Leave `oncotree_code` empty to return mappings for all OncoTree codes
oncotree_to_nci()

# Map a few selected OncoTree codes
oncotree_to_nci(oncotree_code = c('PAOS', 'SCST', 'ITLPDGI', 'SRCCR'))

# Use `expand` to make sure the column `nci_code` is a character vector and
# not a list-column. One-to-many mappings will result in more than row with
# `oncotree_code` values repeated.
oncotree_to_nci(oncotree_code = c('PAOS', 'SCST', 'ITLPDGI', 'SRCCR'), expand
= TRUE)

# Use `keep_empty` to drop or keep one-to-none mappings
oncotree_to_nci(oncotree_code = c('PAOS', 'SCST', 'ITLPDGI', 'SRCCR'), expand
= TRUE, keep_empty = FALSE)

## End(Not run)

---

Map OncoTree to UMLS codes

Description

This function maps OncoTree codes to Unified Medical Language System (UMLS) codes.

Usage

oncotree_to_umls(
  oncotree_code = NULL,
  oncotree_version = "oncotree_latest_stable",
  expand = FALSE,
  keep_empty = TRUE
)

Arguments

oncotree_code	OncoTree codes.
oncotree_version	OncoTree database release version.
expand	Whether to expand one-to-many mappings. If TRUE, one-to-many mappings are expanded into several rows in the output.
keep_empty	OncoTree codes that do not map to UMLS have the umls_code with NA if keep_empty = TRUE. Use keep_empty = FALSE, to remove the mapping (row) altogether from the output.

Value

A tibble of two variables: oncotree_code and umls_code.

Examples

## Not run: 
# Leave `oncotree_code` empty to return mappings for all OncoTree codes
oncotree_to_umls()

# Map a few selected OncoTree codes
oncotree_to_umls(oncotree_code = c('PAOS', 'SCST', 'ITLPDGI', 'SRCCR'))

# Use `expand` to make sure the column `umls_code` is a character vector and
# not a list-column. One-to-many mappings will result in more than row with
# `oncotree_code` values repeated.
oncotree_to_umls(oncotree_code = c('PAOS', 'SCST', 'ITLPDGI', 'SRCCR'),
  expand = TRUE)

# Use `keep_empty` to drop or keep one-to-none mappings
oncotree_to_umls(oncotree_code = c('PAOS', 'SCST', 'ITLPDGI', 'SRCCR'),
  expand = TRUE, keep_empty = FALSE)

## End(Not run)

---

Browse the NCIt

Description

Opens the web browser at NCI Thesaurus for the entries provided as NCI codes.

Usage

open_in_nci_thesaurus(nci_code)

Arguments

nci_code

A character vector of NCI codes.

Value

Run for its side effect.

Examples

## Not run: 
open_in_nci_thesaurus('C3107')

## End(Not run)

---

Map UMLS to OncoTree codes

Description

This function maps Unified Medical Language System (UMLS) codes to OncoTree codes.

Usage

umls_to_oncotree(
  umls_code = NULL,
  oncotree_version = "oncotree_latest_stable",
  expand = FALSE
)

Arguments

umls_code	UMLS codes.
oncotree_version	OncoTree database release version.
expand	Whether to expand one-to-many mappings. If TRUE, one-to-many mappings are expanded into several rows in the output.

Value

A tibble of two variables: umls_code and oncotree_code.

Examples

## Not run: 
# Leave `umls_code` empty to return mappings for all UMLS codes
umls_to_oncotree()

# Map a few selected OncoTree codes
umls_to_oncotree(umls_code = c('C0206642', 'C0600113', 'C0279654', 'C1707436'))

# Use `expand` to make sure the column `oncotree_code` is a character vector and
# not a list-column. One-to-many mappings will result in more than row with
# `oncotree_code` values repeated.
umls_to_oncotree(umls_code = c('C0206642', 'C0600113', 'C0279654', 'C1707436'), expand = TRUE)

## End(Not run)

---