From bbd3b4871ddb103838624163a14be568bb20245b Mon Sep 17 00:00:00 2001 From: allenbaron Date: Fri, 26 Jan 2024 20:18:53 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20DiseaseO?= =?UTF-8?q?ntology/DO.utils@150404e7b79fe8b2e141522663376bbd50f611c5=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pkgdown.yml | 2 +- reference/inventory_omim.html | 19 ++++++++++++----- reference/multimaps.html | 40 +++++++++++++++++++++++------------ reference/read_omim.html | 29 +++++++++++++------------ search.json | 2 +- 5 files changed, 58 insertions(+), 34 deletions(-) diff --git a/pkgdown.yml b/pkgdown.yml index 48e052e..709fe61 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -4,7 +4,7 @@ pkgdown_sha: ~ articles: obtain_use_records: obtain_use_records.html use-reticulate-python: use-reticulate-python.html -last_built: 2024-01-18T22:42Z +last_built: 2024-01-26T20:18Z urls: reference: https://allenbaron.github.io/DO.utils/reference article: https://allenbaron.github.io/DO.utils/articles diff --git a/reference/inventory_omim.html b/reference/inventory_omim.html index d3251bc..02951db 100644 --- a/reference/inventory_omim.html +++ b/reference/inventory_omim.html @@ -62,7 +62,8 @@

Usage onto_path, omim_input, keep_mim = c("#", "%"), - include_hasDbXref = TRUE + include_pred = c("skos:exactMatch", "skos:closeMatch", "oboInOwl:hasDbXref"), + when_pred_NA = "error" ) @@ -86,10 +87,18 @@

ArgumentsOMIM defined MIM symbols are:

MIM symbolMIM type
*gene
+gene, includes phenotype
#phenotype
%phenotype, unknown molecular basis
^deprecated
nonephenotype, suspected/overlap
-
include_hasDbXref
-

Whether oboInOwl:hasDbXref's should be included in -tests for "one-to-multiple" mappings, as a boolean (default: TRUE). -skos:exactMatch & skos:closeMatch mappings are always included.

+
include_pred
+

The predicates to include when testing for one-to-multiple +mappings, as a character vector (default: skos:exactMatch, +skos:closeMatch, and oboInOwl:hasDbXref). All other predicates are +ignored.

+ + +
when_pred_NA
+

What to do when missing predicates are detected, as a +string; one of "error" (default), "warn", or NULL (do nothing). NA +predicates are always ignored when no mapping exists (i.e. one or both +corresponding values of x or y is/are also NA).

diff --git a/reference/multimaps.html b/reference/multimaps.html index 45dc896..ff5de0f 100644 --- a/reference/multimaps.html +++ b/reference/multimaps.html @@ -1,9 +1,7 @@ -Identify One-to-Multiple Mappings — multimaps • DO.utilsIdentify One-to-Multiple Mappings — multimaps • DO.utils @@ -51,14 +49,19 @@
-

Identifies values in x that map to multiple values in y for -skos:exactMatch or skos:closeMatch (and optionally also -oboInOwl:hasDbXref) mapping predicates.

+

Identifies values in x that map to multiple values in y for specified +mapping predicates.

Usage

- 
multimaps(x, pred, y, include_hasDbXref = TRUE)
+ 
multimaps(
+  x,
+  pred,
+  y,
+  include_pred = c("skos:exactMatch", "skos:closeMatch", "oboInOwl:hasDbXref"),
+  when_pred_NA = "error"
+)
@@ -78,10 +81,18 @@

Arguments -
include_hasDbXref
-

Whether oboInOwl:hasDbXref's should be included in -tests for "one-to-multiple" mappings, as a boolean (default: TRUE). -skos:exactMatch & skos:closeMatch mappings are always included.

+
include_pred
+

The predicates to include when testing for one-to-multiple +mappings, as a character vector (default: skos:exactMatch, +skos:closeMatch, and oboInOwl:hasDbXref). All other predicates are +ignored.

+ + +
when_pred_NA
+

What to do when missing predicates are detected, as a +string; one of "error" (default), "warn", or NULL (do nothing). NA +predicates are always ignored when no mapping exists (i.e. one or both +corresponding values of x or y is/are also NA).

@@ -89,7 +100,8 @@

Value

A logical vector specifying the positions in x that map to -multiple values in y.

+multiple values in y. Incomplete mappings, where values of x, y, or +both are NA, are ignored and return FALSE.