1. OmnipathR
  2. man
  3. omnipath_cache_filter_versions.Rd
Browse code

docs rebuild

Türei Dénes authored on 11/04/2021 00:02:55
Showing1 changed files
man/omnipath_cache_filter_versions.Rd
History View file @41d6808
... ... 
@@ -35,7 +35,7 @@ Filters the versions based on multiple conditions: their age and status
35 35 
 # creating an example cache record
36 36 
 bioc_url <- 'https://bioconductor.org/'
37 37 
 version <- omnipath_cache_latest_or_new(url = bioc_url)
38 
-download.file(bioc_url, destfile = version$path)
38 
+httr::GET(bioc_url, httr::write_disk(version$path, overwrite = TRUE))
39 39 
 omnipath_cache_download_ready(version)
40 40 
 record <- dplyr::first(omnipath_cache_search('biocond'))
41 41
Browse code

`post_translational_interactions`: possible to provide `datasets`, not only `exclude`

Türei Dénes authored on 02/04/2021 22:00:20
Showing1 changed files
man/omnipath_cache_filter_versions.Rd
History View file @2e7bce5
... ... 
@@ -26,7 +26,7 @@ versions with `ready` (completed download) status are selected}
26 26 
 }
27 27 
 \value{
28 28 
 Character vector with version IDs, NA if no version satisfies the
29 
-    conditions
29 
+    conditions.
30 30 
 }
31 31 
 \description{
32 32 
 Filters the versions based on multiple conditions: their age and status
Browse code

avoid name collisions between col names and imported package functions

Türei Dénes authored on 11/03/2021 02:06:48
Showing1 changed files
man/omnipath_cache_filter_versions.Rd
History View file @4021df7
... ... 
@@ -40,7 +40,7 @@ omnipath_cache_download_ready(version)
40 40 
 record <- dplyr::first(omnipath_cache_search('biocond'))
41 41
42 42 
 # only the versions with status "ready"
43 
-version_numbers <- omnipath_cache_filter_versions(status = 'ready')
43 
+version_numbers <- omnipath_cache_filter_versions(record, status = 'ready')
44 44 
 omnipath_cache_remove(url = bioc_url) # cleaning up
45 45
46 46 
 }
Browse code

runnable examples whereever it's possible

Türei Dénes authored on 10/03/2021 23:06:36
Showing1 changed files
man/omnipath_cache_filter_versions.Rd
History View file @be9cdd4
... ... 
@@ -32,10 +32,15 @@ Character vector with version IDs, NA if no version satisfies the
32 32 
 Filters the versions based on multiple conditions: their age and status
33 33 
 }
34 34 
 \examples{
35 
-\donttest{
35 
+# creating an example cache record
36 
+bioc_url <- 'https://bioconductor.org/'
37 
+version <- omnipath_cache_latest_or_new(url = bioc_url)
38 
+download.file(bioc_url, destfile = version$path)
39 
+omnipath_cache_download_ready(version)
36 40 
 record <- dplyr::first(omnipath_cache_search('biocond'))
41 
+
37 42 
 # only the versions with status "ready"
38 43 
 version_numbers <- omnipath_cache_filter_versions(status = 'ready')
39 
-}
44 
+omnipath_cache_remove(url = bioc_url) # cleaning up
40 45
41 46 
 }
Browse code

docs: added all missing return values

Türei Dénes authored on 10/03/2021 18:45:04
Showing1 changed files
man/omnipath_cache_filter_versions.Rd
History View file @9ae0bbd
... ... 
@@ -26,7 +26,7 @@ versions with `ready` (completed download) status are selected}
26 26 
 }
27 27 
 \value{
28 28 
 Character vector with version IDs, NA if no version satisfies the
29 
-conditions
29 
+    conditions
30 30 
 }
31 31 
 \description{
32 32 
 Filters the versions based on multiple conditions: their age and status
Browse code

regenerated website (not sure if successful)

Türei Dénes authored on 10/03/2021 17:50:07
Showing1 changed files
man/omnipath_cache_filter_versions.Rd
History View file @af0ed3d
... ... 
@@ -33,7 +33,7 @@ Filters the versions based on multiple conditions: their age and status
33 33 
 }
34 34 
 \examples{
35 35 
 \donttest{
36 
-record <- omnipath_cache_search('biocond') \%>\% dplyr::first
36 
+record <- dplyr::first(omnipath_cache_search('biocond'))
37 37 
 # only the versions with status "ready"
38 38 
 version_numbers <- omnipath_cache_filter_versions(status = 'ready')
39 39 
 }
Browse code

added new man pages

Türei Dénes authored on 10/03/2021 14:32:26
Showing1 changed files
man/omnipath_cache_filter_versions.Rd
History View file @17c08fe
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,41 @@
1 
+% Generated by roxygen2: do not edit by hand
2 
+% Please edit documentation in R/cache.R
3 
+\name{omnipath_cache_filter_versions}
4 
+\alias{omnipath_cache_filter_versions}
5 
+\title{Filters the versions from one cache record}
6 
+\usage{
7 
+omnipath_cache_filter_versions(
8 
+  record,
9 
+  latest = FALSE,
10 
+  max_age = NULL,
11 
+  min_age = NULL,
12 
+  status = CACHE_STATUS$READY
13 
+)
14 
+}
15 
+\arguments{
16 
+\item{record}{A cache record}
17 
+
18 
+\item{latest}{Return the most recent version}
19 
+
20 
+\item{max_age}{The maximum age in days (e.g. 5: 5 days old or more recent)}
21 
+
22 
+\item{min_age}{The minimum age in days (e.g. 5: 5 days old or older)}
23 
+
24 
+\item{status}{Character vector with status codes. By default only the
25 
+versions with `ready` (completed download) status are selected}
26 
+}
27 
+\value{
28 
+Character vector with version IDs, NA if no version satisfies the
29 
+conditions
30 
+}
31 
+\description{
32 
+Filters the versions based on multiple conditions: their age and status
33 
+}
34 
+\examples{
35 
+\donttest{
36 
+record <- omnipath_cache_search('biocond') \%>\% dplyr::first
37 
+# only the versions with status "ready"
38 
+version_numbers <- omnipath_cache_filter_versions(status = 'ready')
39 
+}
40 
+
41 
+}