gen_tibble loci=example_loci,
backingfile = tempfile())
#>
-#> gen_tibble saved to /tmp/RtmpCN89XW/file1fe22d3155fa.gt
-#> using bigSNP file: /tmp/RtmpCN89XW/file1fe22d3155fa.rds
-#> with backing file: /tmp/RtmpCN89XW/file1fe22d3155fa.bk
+#> gen_tibble saved to /tmp/RtmpYea289/file20212c4ee04.gt
+#> using bigSNP file: /tmp/RtmpYea289/file20212c4ee04.rds
+#> with backing file: /tmp/RtmpYea289/file20212c4ee04.bk
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/RtmpCN89XW/file1fe22d3155fa.gt')
+#> gt_load('/tmp/RtmpYea289/file20212c4ee04.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 @@ -535,16 +535,15 @@
gt_file_name <- gt_save(example_gt)
#>
-#> gen_tibble saved to /tmp/RtmpCN89XW/file1fe22d3155fa.gt
-#> using bigSNP file: /tmp/RtmpCN89XW/file1fe22d3155fa.rds
-#> with backing file: /tmp/RtmpCN89XW/file1fe22d3155fa.bk
+#> gen_tibble saved to /tmp/RtmpYea289/file20212c4ee04.gt
+#> using bigSNP file: /tmp/RtmpYea289/file20212c4ee04.rds
+#> with backing file: /tmp/RtmpYea289/file20212c4ee04.bk
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/RtmpCN89XW/file1fe22d3155fa.gt')
+#> gt_load('/tmp/RtmpYea289/file20212c4ee04.gt')
gt_file_name
-#> [1] "/tmp/RtmpCN89XW/file1fe22d3155fa.gt"
-#> [2] "/tmp/RtmpCN89XW/file1fe22d3155fa.rds"
-#> [3] "/tmp/RtmpCN89XW/file1fe22d3155fa.bk"
+#> [1] "/tmp/RtmpYea289/file20212c4ee04.gt" "/tmp/RtmpYea289/file20212c4ee04.rds"
+#> [3] "/tmp/RtmpYea289/file20212c4ee04.bk"
In a later session, we could reload the data with:
new_example_gt <- gt_load(gt_file_name[1])
@@ -568,12 +567,12 @@ 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/RtmpCN89XW/pop_a_1fe2676886c2.gt
-#> using bigSNP file: /tmp/RtmpCN89XW/pop_a_1fe2676886c2.rds
-#> with backing file: /tmp/RtmpCN89XW/pop_a_1fe2676886c2.bk
+#> gen_tibble saved to /tmp/RtmpYea289/pop_a_202117bdf31.gt
+#> using bigSNP file: /tmp/RtmpYea289/pop_a_202117bdf31.rds
+#> with backing file: /tmp/RtmpYea289/pop_a_202117bdf31.bk
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/RtmpCN89XW/pop_a_1fe2676886c2.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
@@ -589,7 +588,7 @@
gt_as_plink(example_gt, file = tempfile("new_bed_"))
-#> [1] "/tmp/RtmpCN89XW/new_bed_1fe22a9cffd0.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
@@ -623,22 +622,22 @@
And inspect them:
+#> gt_load('/tmp/RtmpYea289/gt_merged.gt')Let’s check the resulting gen_tibble:
merged_gt
@@ -773,12 +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/RtmpCN89XW/missing_1fe23b55f45.gt
-#> using bigSNP file: /tmp/RtmpCN89XW/missing_1fe23b55f45.rds
-#> with backing file: /tmp/RtmpCN89XW/missing_1fe23b55f45.bk
+#> gen_tibble saved to /tmp/RtmpYea289/missing_20213f03c54f.gt
+#> using bigSNP file: /tmp/RtmpYea289/missing_20213f03c54f.rds
+#> with backing file: /tmp/RtmpYea289/missing_20213f03c54f.bk
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/RtmpCN89XW/missing_1fe23b55f45.gt')
+#> gt_load('/tmp/RtmpYea289/missing_20213f03c54f.gt')
missing_gt
#> # A gen_tibble: 500 loci
#> # A tibble: 200 × 3
diff --git a/articles/a02_qc.html b/articles/a02_qc.html
index 6c681fe3..661221ec 100644
--- a/articles/a02_qc.html
+++ b/articles/a02_qc.html
@@ -316,15 +316,15 @@ Save
##
-## gen_tibble saved to /tmp/RtmpcxfaGM/file203214d46880.gt
-## using bigSNP file: /tmp/RtmpcxfaGM/file20325b7c826a.rds
-## with backing file: /tmp/RtmpcxfaGM/file20325b7c826a.bk
+## gen_tibble saved to /tmp/RtmpDgULOM/file20752545631f.gt
+## using bigSNP file: /tmp/RtmpDgULOM/file20757d31544b.rds## with backing file: /tmp/RtmpDgULOM/file20757d31544b.bk## make sure that you do NOT delete those files!## to reload the gen_tibble in another session, use:## gt_load('/tmp/RtmpcxfaGM/file203214d46880.gt')## [1] "/tmp/RtmpcxfaGM/file203214d46880.gt"
-## [2] "/tmp/RtmpcxfaGM/file20325b7c826a.rds"
-## [3] "/tmp/RtmpcxfaGM/file20325b7c826a.bk"## gt_load('/tmp/RtmpDgULOM/file20752545631f.gt')## [1] "/tmp/RtmpDgULOM/file20752545631f.gt"
+## [2] "/tmp/RtmpDgULOM/file20757d31544b.rds"
+## [3] "/tmp/RtmpDgULOM/file20757d31544b.bk"
geno_file <- gt_as_geno_lea(anole_gt)
geno_file
-#> [1] "/tmp/Rtmp8ZVyLK/anolis_207319ed399b.geno"
+#> [1] "/tmp/RtmptyAaU4/anolis_20b8d3b88ff.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