From b9790cc7b0b87808c12c49240a377cc377c067be Mon Sep 17 00:00:00 2001 From: Hajk-Georg Drost Date: Sat, 2 Dec 2023 15:45:08 +0100 Subject: [PATCH] update docs --- docs/articles/BioMart_Examples.html | 2 +- docs/articles/Database_Retrieval.html | 2 +- docs/articles/Functional_Annotation.html | 2 +- docs/articles/MetaGenome_Retrieval.html | 2 +- docs/articles/Sequence_Retrieval.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/cachedir.html | 2 +- docs/reference/cachedir_set.html | 4 ++-- man/getBio.Rd | 2 +- man/getBioSet.Rd | 2 +- man/getCollection.Rd | 2 +- man/getGenome.Rd | 2 +- man/getGenomeSet.Rd | 2 +- man/getRNA.Rd | 2 +- 14 files changed, 15 insertions(+), 15 deletions(-) diff --git a/docs/articles/BioMart_Examples.html b/docs/articles/BioMart_Examples.html index 48502ef..35f7d89 100644 --- a/docs/articles/BioMart_Examples.html +++ b/docs/articles/BioMart_Examples.html @@ -92,7 +92,7 @@

Ensembl BioMart Examples

-

2023-12-01

+

2023-12-02

Source: vignettes/BioMart_Examples.Rmd diff --git a/docs/articles/Database_Retrieval.html b/docs/articles/Database_Retrieval.html index 0599d75..9e5906a 100644 --- a/docs/articles/Database_Retrieval.html +++ b/docs/articles/Database_Retrieval.html @@ -92,7 +92,7 @@

NCBI Database Retrieval

-

2023-12-01

+

2023-12-02

Source: vignettes/Database_Retrieval.Rmd diff --git a/docs/articles/Functional_Annotation.html b/docs/articles/Functional_Annotation.html index 2b905e5..53969bf 100644 --- a/docs/articles/Functional_Annotation.html +++ b/docs/articles/Functional_Annotation.html @@ -92,7 +92,7 @@

Functional Annotation with biomartr

-

2023-12-01

+

2023-12-02

Source: vignettes/Functional_Annotation.Rmd diff --git a/docs/articles/MetaGenome_Retrieval.html b/docs/articles/MetaGenome_Retrieval.html index 059c97d..cc76b35 100644 --- a/docs/articles/MetaGenome_Retrieval.html +++ b/docs/articles/MetaGenome_Retrieval.html @@ -92,7 +92,7 @@

Meta-Genome Retrieval

-

2023-12-01

+

2023-12-02

Source: vignettes/MetaGenome_Retrieval.Rmd diff --git a/docs/articles/Sequence_Retrieval.html b/docs/articles/Sequence_Retrieval.html index 47b8a15..37a36f0 100644 --- a/docs/articles/Sequence_Retrieval.html +++ b/docs/articles/Sequence_Retrieval.html @@ -92,7 +92,7 @@

Sequence Retrieval

-

2023-12-01

+

2023-12-02

Source: vignettes/Sequence_Retrieval.Rmd diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9775c43..b4847b5 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -7,5 +7,5 @@ articles: Functional_Annotation: Functional_Annotation.html MetaGenome_Retrieval: MetaGenome_Retrieval.html Sequence_Retrieval: Sequence_Retrieval.html -last_built: 2023-12-01T12:16Z +last_built: 2023-12-02T14:42Z diff --git a/docs/reference/cachedir.html b/docs/reference/cachedir.html index 4081439..9f37f2f 100644 --- a/docs/reference/cachedir.html +++ b/docs/reference/cachedir.html @@ -100,7 +100,7 @@

See also

Examples

cachedir()
-#> [1] "/var/folders/yn/mgwl8_b56hz4v2c2vlfxj07w00076j/T//RtmpZiYibX"
+#> [1] "/var/folders/yn/mgwl8_b56hz4v2c2vlfxj07w00076j/T//Rtmp3umua6"
diff --git a/docs/reference/cachedir_set.html b/docs/reference/cachedir_set.html index a2a43ea..8d2210c 100644 --- a/docs/reference/cachedir_set.html +++ b/docs/reference/cachedir_set.html @@ -100,10 +100,10 @@

See also

Examples

# By default it is tempdir()
 cachedir()
-#> [1] "/var/folders/yn/mgwl8_b56hz4v2c2vlfxj07w00076j/T//RtmpZiYibX"
+#> [1] "/var/folders/yn/mgwl8_b56hz4v2c2vlfxj07w00076j/T//Rtmp3umua6"
 # cachedir_set("~/Bio_data/biomartr_cache/")
 cachedir()
-#> [1] "/var/folders/yn/mgwl8_b56hz4v2c2vlfxj07w00076j/T//RtmpZiYibX"
+#> [1] "/var/folders/yn/mgwl8_b56hz4v2c2vlfxj07w00076j/T//Rtmp3umua6"
diff --git a/man/getBio.Rd b/man/getBio.Rd index 4574743..7b7eb86 100644 --- a/man/getBio.Rd +++ b/man/getBio.Rd @@ -79,7 +79,7 @@ If the primary assembly file is not present for a species that indicates that there were no haplotype/patch regions, and in such cases, the 'toplevel file is used. For more details see: -\\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} +\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} \item{format}{"gff3", alternative "gtf" for ensembl.} diff --git a/man/getBioSet.Rd b/man/getBioSet.Rd index 665649c..d2c2907 100644 --- a/man/getBioSet.Rd +++ b/man/getBioSet.Rd @@ -80,7 +80,7 @@ If the primary assembly file is not present for a species that indicates that there were no haplotype/patch regions, and in such cases, the 'toplevel file is used. For more details see: -\\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} +\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} \item{format}{"gff3", alternative "gtf" for ensembl.} diff --git a/man/getCollection.Rd b/man/getCollection.Rd index dabdea5..4acc786 100644 --- a/man/getCollection.Rd +++ b/man/getCollection.Rd @@ -58,7 +58,7 @@ If the primary assembly file is not present for a species that indicates that there were no haplotype/patch regions, and in such cases, the 'toplevel file is used. For more details see: -\\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} +\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} \item{analyse_genome}{logical, default FALSE. If TRUE, get general genome statistics like gc content etc. For more details, see ?summary_genome} diff --git a/man/getGenome.Rd b/man/getGenome.Rd index 5d9a2c0..972e339 100644 --- a/man/getGenome.Rd +++ b/man/getGenome.Rd @@ -61,7 +61,7 @@ If the primary assembly file is not present for a species that indicates that there were no haplotype/patch regions, and in such cases, the 'toplevel file is used. For more details see: -\\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} +\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} \item{mute_citation}{logical, default FALSE, indicating whether citation message should be muted.} diff --git a/man/getGenomeSet.Rd b/man/getGenomeSet.Rd index b8553bb..4db0e9e 100644 --- a/man/getGenomeSet.Rd +++ b/man/getGenomeSet.Rd @@ -62,7 +62,7 @@ If the primary assembly file is not present for a species that indicates that there were no haplotype/patch regions, and in such cases, the 'toplevel file is used. For more details see: -\\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} +\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} \item{mute_citation}{logical, default FALSE, indicating whether citation message should be muted.} } diff --git a/man/getRNA.Rd b/man/getRNA.Rd index cc8ea49..45d24a9 100644 --- a/man/getRNA.Rd +++ b/man/getRNA.Rd @@ -56,7 +56,7 @@ If the primary assembly file is not present for a species that indicates that there were no haplotype/patch regions, and in such cases, the 'toplevel file is used. For more details see: -\\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} +\href{https://grch37.ensembl.org/info/genome/genebuild/assembly.html}{ensembl tutorial}} \item{path}{a character string specifying the location (a folder) in which the corresponding