gen_tibble loci=example_loci,
backingfile = tempfile())
#>
-#> gen_tibble saved to /tmp/RtmpDE6HJM/file1c672975fe5d.gt
-#> using bigSNP file: /tmp/RtmpDE6HJM/file1c672975fe5d.rds
-#> with backing file: /tmp/RtmpDE6HJM/file1c672975fe5d.bk
+#> gen_tibble saved to /tmp/Rtmpj7B9jK/file1c6d4e60e545.gt
+#> using bigSNP file: /tmp/Rtmpj7B9jK/file1c6d4e60e545.rds
+#> with backing file: /tmp/Rtmpj7B9jK/file1c6d4e60e545.bk
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/RtmpDE6HJM/file1c672975fe5d.gt')
+#> gt_load('/tmp/Rtmpj7B9jK/file1c6d4e60e545.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 @@
gt_file_name <- gt_save(example_gt)
#>
-#> gen_tibble saved to /tmp/RtmpDE6HJM/file1c672975fe5d.gt
-#> using bigSNP file: /tmp/RtmpDE6HJM/file1c672975fe5d.rds
-#> with backing file: /tmp/RtmpDE6HJM/file1c672975fe5d.bk
+#> gen_tibble saved to /tmp/Rtmpj7B9jK/file1c6d4e60e545.gt
+#> using bigSNP file: /tmp/Rtmpj7B9jK/file1c6d4e60e545.rds
+#> with backing file: /tmp/Rtmpj7B9jK/file1c6d4e60e545.bk
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/RtmpDE6HJM/file1c672975fe5d.gt')
+#> gt_load('/tmp/Rtmpj7B9jK/file1c6d4e60e545.gt')
gt_file_name
-#> [1] "/tmp/RtmpDE6HJM/file1c672975fe5d.gt"
-#> [2] "/tmp/RtmpDE6HJM/file1c672975fe5d.rds"
-#> [3] "/tmp/RtmpDE6HJM/file1c672975fe5d.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/RtmpDE6HJM/pop_a_1c67541d18eb.gt
-#> using bigSNP file: /tmp/RtmpDE6HJM/pop_a_1c67541d18eb.rds
-#> with backing file: /tmp/RtmpDE6HJM/pop_a_1c67541d18eb.bk
+#> 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
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/RtmpDE6HJM/pop_a_1c67541d18eb.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 @@
gt_as_plink(example_gt, file = tempfile("new_bed_"))
-#> [1] "/tmp/RtmpDE6HJM/new_bed_1c6757c2534e.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 @@
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/RtmpDE6HJM/pop_b_1c6755534058.gt
-#> using bigSNP file: /tmp/RtmpDE6HJM/pop_b_1c6755534058.rds
-#> with backing file: /tmp/RtmpDE6HJM/pop_b_1c6755534058.bk
+#> 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
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/RtmpDE6HJM/pop_b_1c6755534058.gt')And inspect them:
+#> gt_load('/tmp/Rtmpj7B9jK/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/RtmpDE6HJM/missing_1c672b4e6eba.gt
-#> using bigSNP file: /tmp/RtmpDE6HJM/missing_1c672b4e6eba.rds
-#> with backing file: /tmp/RtmpDE6HJM/missing_1c672b4e6eba.bk
+#> 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
#> make sure that you do NOT delete those files!
#> to reload the gen_tibble in another session, use:
-#> gt_load('/tmp/RtmpDE6HJM/missing_1c672b4e6eba.gt')
missing_gt
#> # A gen_tibble: 500 loci
diff --git a/articles/a02_qc.html b/articles/a02_qc.html
index bf434575..1fed3fa1 100644
--- a/articles/a02_qc.html
+++ b/articles/a02_qc.html
@@ -318,15 +318,15 @@ Save
##
-## gen_tibble saved to /tmp/RtmppUmng6/file1cb755cf787a.gt
-## using bigSNP file: /tmp/RtmppUmng6/file1cb7585253e8.rds
-## with backing file: /tmp/RtmppUmng6/file1cb7585253e8.bk
+## gen_tibble saved to /tmp/RtmpSsxRha/file1cc11b90e7e3.gt
+## using bigSNP file: /tmp/RtmpSsxRha/file1cc13b5c8e39.rds## with backing file: /tmp/RtmpSsxRha/file1cc13b5c8e39.bk## make sure that you do NOT delete those files!## to reload the gen_tibble in another session, use:## gt_load('/tmp/RtmppUmng6/file1cb755cf787a.gt')## [1] "/tmp/RtmppUmng6/file1cb755cf787a.gt"
-## [2] "/tmp/RtmppUmng6/file1cb7585253e8.rds"
-## [3] "/tmp/RtmppUmng6/file1cb7585253e8.bk"## gt_load('/tmp/RtmpSsxRha/file1cc11b90e7e3.gt')## [1] "/tmp/RtmpSsxRha/file1cc11b90e7e3.gt"
+## [2] "/tmp/RtmpSsxRha/file1cc13b5c8e39.rds"
+## [3] "/tmp/RtmpSsxRha/file1cc13b5c8e39.bk"
geno_file <- gt_as_geno_lea(anole_gt)
geno_file
-#> [1] "/tmp/Rtmpr542f2/anolis_1cf7586610e.geno"
+#> [1] "/tmp/RtmpzjPc5H/anolis_1d0265e15d91.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