diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index 3940a15f..c8ec8f98 100644 Binary files a/apple-touch-icon-120x120.png and b/apple-touch-icon-120x120.png differ diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png index 8ca73be6..857249b4 100644 Binary files a/apple-touch-icon-152x152.png and b/apple-touch-icon-152x152.png differ diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index 940b653e..5f528965 100644 Binary files a/apple-touch-icon-180x180.png and b/apple-touch-icon-180x180.png differ diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 87fe88f5..f6cb2e56 100644 Binary files a/apple-touch-icon-60x60.png and b/apple-touch-icon-60x60.png differ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png index 9b91470e..d141b9dc 100644 Binary files a/apple-touch-icon-76x76.png and b/apple-touch-icon-76x76.png differ diff --git a/apple-touch-icon.png b/apple-touch-icon.png index 9fa9f59b..4761a1e8 100644 Binary files a/apple-touch-icon.png and b/apple-touch-icon.png differ diff --git a/articles/a01_overview.html b/articles/a01_overview.html index bfda54d6..a2bcf822 100644 --- a/articles/a01_overview.html +++ b/articles/a01_overview.html @@ -191,12 +191,12 @@

The gen_tibble loci=example_loci, backingfile = tempfile()) #> -#> gen_tibble saved to /tmp/Rtmpj7B9jK/file1c6d4e60e545.gt -#> using bigSNP file: /tmp/Rtmpj7B9jK/file1c6d4e60e545.rds -#> with backing file: /tmp/Rtmpj7B9jK/file1c6d4e60e545.bk +#> gen_tibble saved to /tmp/RtmpVezwmf/file1c9e7a491260.gt +#> using bigSNP file: /tmp/RtmpVezwmf/file1c9e7a491260.rds +#> with backing file: /tmp/RtmpVezwmf/file1c9e7a491260.bk #> make sure that you do NOT delete those files! #> to reload the gen_tibble in another session, use: -#> gt_load('/tmp/Rtmpj7B9jK/file1c6d4e60e545.gt') +#> gt_load('/tmp/RtmpVezwmf/file1c9e7a491260.gt')

We are provided information on where the three files underlying the genotype information are stored. As we don’t want to keep the files, we used the tmp directory; normally you will want to use your working @@ -538,17 +538,17 @@

Saving and reading data
 gt_file_name <- gt_save(example_gt)
 #> 
-#> gen_tibble saved to /tmp/Rtmpj7B9jK/file1c6d4e60e545.gt
-#> using bigSNP file: /tmp/Rtmpj7B9jK/file1c6d4e60e545.rds
-#> with backing file: /tmp/Rtmpj7B9jK/file1c6d4e60e545.bk
+#> gen_tibble saved to /tmp/RtmpVezwmf/file1c9e7a491260.gt
+#> using bigSNP file: /tmp/RtmpVezwmf/file1c9e7a491260.rds
+#> with backing file: /tmp/RtmpVezwmf/file1c9e7a491260.bk
 #> make sure that you do NOT delete those files!
 #> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/Rtmpj7B9jK/file1c6d4e60e545.gt')
+#> gt_load('/tmp/RtmpVezwmf/file1c9e7a491260.gt') 
 gt_file_name
-#> [1] "/tmp/Rtmpj7B9jK/file1c6d4e60e545.gt" 
-#> [2] "/tmp/Rtmpj7B9jK/file1c6d4e60e545.rds"
-#> [3] "/tmp/Rtmpj7B9jK/file1c6d4e60e545.bk"
+#> [1] "/tmp/RtmpVezwmf/file1c9e7a491260.gt" +#> [2] "/tmp/RtmpVezwmf/file1c9e7a491260.rds" +#> [3] "/tmp/RtmpVezwmf/file1c9e7a491260.bk"

In a later session, we could reload the data with:

 new_example_gt <- gt_load(gt_file_name[1])
@@ -572,12 +572,12 @@ 
Saving and reading databed_path_pop_a <- system.file("extdata/pop_a.bed", package = "tidypopgen")
 pop_a_gt <- gen_tibble(bed_path_pop_a, backingfile = tempfile("pop_a_"))
 #> 
-#> gen_tibble saved to /tmp/Rtmpj7B9jK/pop_a_1c6d75a116b1.gt
-#> using bigSNP file: /tmp/Rtmpj7B9jK/pop_a_1c6d75a116b1.rds
-#> with backing file: /tmp/Rtmpj7B9jK/pop_a_1c6d75a116b1.bk
+#> gen_tibble saved to /tmp/RtmpVezwmf/pop_a_1c9e60a1d7cb.gt
+#> using bigSNP file: /tmp/RtmpVezwmf/pop_a_1c9e60a1d7cb.rds
+#> with backing file: /tmp/RtmpVezwmf/pop_a_1c9e60a1d7cb.bk
 #> make sure that you do NOT delete those files!
 #> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/Rtmpj7B9jK/pop_a_1c6d75a116b1.gt')
+#> gt_load('/tmp/RtmpVezwmf/pop_a_1c9e60a1d7cb.gt')

For this vignette, we don’t want to keep files, so we are using again a temporary path for the backing files, but in normal instances, we can simply omit the backingfile parameter, and the @@ -593,7 +593,7 @@

Saving and reading data 
 gt_as_plink(example_gt, file =  tempfile("new_bed_"))
-#> [1] "/tmp/Rtmpj7B9jK/new_bed_1c6d43bd0bdb.bed"
+#> [1] "/tmp/RtmpVezwmf/new_bed_1c9e12fd19e5.bed"

This will also write a .bim and .fam file and save them together with the .bed file. Note that, from the main tibble, only id, population and sex will be preserved in the @@ -627,23 +627,23 @@

Merging databigsnp_path_a <- bigsnpr::snp_readBed(bed_path_pop_a, backingfile = tempfile("pop_a_")) pop_a_gt <- gen_tibble(bigsnp_path_a) #> -#> gen_tibble saved to /tmp/Rtmpj7B9jK/pop_a_1c6d44e0c25f.gt -#> using bigSNP file: /tmp/Rtmpj7B9jK/pop_a_1c6d44e0c25f.rds -#> with backing file: /tmp/Rtmpj7B9jK/pop_a_1c6d44e0c25f.bk +#> gen_tibble saved to /tmp/RtmpVezwmf/pop_a_1c9edd1d7c4.gt +#> using bigSNP file: /tmp/RtmpVezwmf/pop_a_1c9edd1d7c4.rds +#> with backing file: /tmp/RtmpVezwmf/pop_a_1c9edd1d7c4.bk #> make sure that you do NOT delete those files! #> to reload the gen_tibble in another session, use: -#> gt_load('/tmp/Rtmpj7B9jK/pop_a_1c6d44e0c25f.gt') +#> gt_load('/tmp/RtmpVezwmf/pop_a_1c9edd1d7c4.gt') 
 bed_path_pop_b <- system.file("extdata/pop_b.bed", package = "tidypopgen")
 bigsnp_path_b <- bigsnpr::snp_readBed(bed_path_pop_b, backingfile =  tempfile("pop_b_"))
 pop_b_gt <- gen_tibble(bigsnp_path_b)
 #> 
-#> gen_tibble saved to /tmp/Rtmpj7B9jK/pop_b_1c6d24b9f445.gt
-#> using bigSNP file: /tmp/Rtmpj7B9jK/pop_b_1c6d24b9f445.rds
-#> with backing file: /tmp/Rtmpj7B9jK/pop_b_1c6d24b9f445.bk
+#> gen_tibble saved to /tmp/RtmpVezwmf/pop_b_1c9e50b4a1ed.gt
+#> using bigSNP file: /tmp/RtmpVezwmf/pop_b_1c9e50b4a1ed.rds
+#> with backing file: /tmp/RtmpVezwmf/pop_b_1c9e50b4a1ed.bk
 #> make sure that you do NOT delete those files!
 #> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/Rtmpj7B9jK/pop_b_1c6d24b9f445.gt')
+#> gt_load('/tmp/RtmpVezwmf/pop_b_1c9e50b4a1ed.gt')

And inspect them:

 pop_a_gt
@@ -712,12 +712,12 @@ 
Merging data#> ( 5 were flipped to match the reference set)
 #> ( 2 are ambiguous, of which 2 were removed)
 #> 
-#> gen_tibble saved to /tmp/Rtmpj7B9jK/gt_merged.gt
-#> using bigSNP file: /tmp/Rtmpj7B9jK/gt_merged.rds
-#> with backing file: /tmp/Rtmpj7B9jK/gt_merged.bk
+#> gen_tibble saved to /tmp/RtmpVezwmf/gt_merged.gt
+#> using bigSNP file: /tmp/RtmpVezwmf/gt_merged.rds
+#> with backing file: /tmp/RtmpVezwmf/gt_merged.bk
 #> make sure that you do NOT delete those files!
 #> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/Rtmpj7B9jK/gt_merged.gt')
+#> gt_load('/tmp/RtmpVezwmf/gt_merged.gt')

Let’s check the resulting gen_tibble:

 merged_gt
@@ -772,12 +772,12 @@ 
Imputationbed_file <- system.file("extdata", "example-missing.bed", package = "bigsnpr")
 missing_gt <- gen_tibble(bed_file,  backingfile = tempfile("missing_"))
 #> 
-#> gen_tibble saved to /tmp/Rtmpj7B9jK/missing_1c6d50940733.gt
-#> using bigSNP file: /tmp/Rtmpj7B9jK/missing_1c6d50940733.rds
-#> with backing file: /tmp/Rtmpj7B9jK/missing_1c6d50940733.bk
+#> gen_tibble saved to /tmp/RtmpVezwmf/missing_1c9e40e09379.gt
+#> using bigSNP file: /tmp/RtmpVezwmf/missing_1c9e40e09379.rds
+#> with backing file: /tmp/RtmpVezwmf/missing_1c9e40e09379.bk
 #> make sure that you do NOT delete those files!
 #> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/Rtmpj7B9jK/missing_1c6d50940733.gt')
+#> gt_load('/tmp/RtmpVezwmf/missing_1c9e40e09379.gt') 
 missing_gt
 #> # A gen_tibble: 500 loci
diff --git a/articles/a02_qc.html b/articles/a02_qc.html
index 1fed3fa1..461cdeb6 100644
--- a/articles/a02_qc.html
+++ b/articles/a02_qc.html
@@ -318,15 +318,15 @@ 
Save
 
 gt_save(ld_data, file_name = tempfile())

 
## 
-## gen_tibble saved to /tmp/RtmpSsxRha/file1cc11b90e7e3.gt

-
## using bigSNP file: /tmp/RtmpSsxRha/file1cc13b5c8e39.rds

-
## with backing file: /tmp/RtmpSsxRha/file1cc13b5c8e39.bk

+## gen_tibble saved to /tmp/RtmpXQUBwh/file1cef30b62337.gt
+
## using bigSNP file: /tmp/RtmpXQUBwh/file1cef3d3bfd08.rds
+
## with backing file: /tmp/RtmpXQUBwh/file1cef3d3bfd08.bk
## make sure that you do NOT delete those files!
## to reload the gen_tibble in another session, use:
-
## gt_load('/tmp/RtmpSsxRha/file1cc11b90e7e3.gt')
-
## [1] "/tmp/RtmpSsxRha/file1cc11b90e7e3.gt" 
-## [2] "/tmp/RtmpSsxRha/file1cc13b5c8e39.rds"
-## [3] "/tmp/RtmpSsxRha/file1cc13b5c8e39.bk"
+
## gt_load('/tmp/RtmpXQUBwh/file1cef30b62337.gt')
+
## [1] "/tmp/RtmpXQUBwh/file1cef30b62337.gt" 
+## [2] "/tmp/RtmpXQUBwh/file1cef3d3bfd08.rds"
+## [3] "/tmp/RtmpXQUBwh/file1cef3d3bfd08.bk"
diff --git a/articles/a03_example_clustering_and_dapc.html b/articles/a03_example_clustering_and_dapc.html index 627d0370..a5eaea51 100644 --- a/articles/a03_example_clustering_and_dapc.html +++ b/articles/a03_example_clustering_and_dapc.html @@ -476,7 +476,7 @@

Clustering with sNMF
 geno_file <- gt_as_geno_lea(anole_gt)
 geno_file
-#> [1] "/tmp/RtmpzjPc5H/anolis_1d0265e15d91.geno"
+#> [1] "/tmp/RtmpkhyaE3/anolis_1d306a9d2e8f.geno"

Note that the .geno file is placed by default in the same directory and using the same name as the backing file of the gen_tibble

diff --git a/favicon-16x16.png b/favicon-16x16.png index 9012deee..172d32b9 100644 Binary files a/favicon-16x16.png and b/favicon-16x16.png differ diff --git a/favicon-32x32.png b/favicon-32x32.png index 129765c3..a2c3d9db 100644 Binary files a/favicon-32x32.png and b/favicon-32x32.png differ diff --git a/favicon.ico b/favicon.ico index 862b61b5..03940f6d 100644 Binary files a/favicon.ico and b/favicon.ico differ diff --git a/pkgdown.yml b/pkgdown.yml index e5cf494a..a97f953d 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,5 +6,5 @@ articles: a02_qc: a02_qc.html a03_example_clustering_and_dapc: a03_example_clustering_and_dapc.html a99_plink_cheatsheet: a99_plink_cheatsheet.html -last_built: 2024-06-13T21:31Z +last_built: 2024-06-13T21:36Z