diff --git a/inst/extdata/pop_a_ped_plink.log b/inst/extdata/pop_a_ped_plink.log new file mode 100644 index 00000000..8195b484 --- /dev/null +++ b/inst/extdata/pop_a_ped_plink.log @@ -0,0 +1,24 @@ +PLINK v1.90b7.2 64-bit (11 Dec 2023) +Options in effect: + --bfile C:/Users/eviec/Git/tidypopgen/inst/extdata/pop_a + --out C:/Users/eviec/Git/tidypopgen/inst/extdata/pop_a_ped_plink + --recode + +Hostname: LAPTOP-S7R1KB1T +Working directory: C:\Users\eviec\OneDrive\Desktop\PhD\tidypopgen\ped_check +Start time: Fri May 10 06:29:41 2024 + +Random number seed: 1715318981 +8080 MB RAM detected; reserving 4040 MB for main workspace. +16 variants loaded from .bim file. +5 people (5 males, 0 females) loaded from .fam. +Using 1 thread (no multithreaded calculations invoked). +Before main variant filters, 5 founders and 0 nonfounders present. +Calculating allele frequencies... done. +Total genotyping rate is exactly 1. +16 variants and 5 people pass filters and QC. +Note: No phenotypes present. +--recode ped to C:/Users/eviec/Git/tidypopgen/inst/extdata/pop_a_ped_plink.ped ++ C:/Users/eviec/Git/tidypopgen/inst/extdata/pop_a_ped_plink.map ... done. + +End time: Fri May 10 06:29:41 2024 diff --git a/inst/extdata/pop_a_ped_plink.map b/inst/extdata/pop_a_ped_plink.map new file mode 100644 index 00000000..5d4cd2d3 --- /dev/null +++ b/inst/extdata/pop_a_ped_plink.map @@ -0,0 +1,16 @@ +1 rs4477212 0 82154 +1 rs3094315 0 752566 +1 rs3131972 0 752721 +1 rs12124819 0 776546 +1 rs11240777 0 798959 +1 rs1110052 0 873558 +1 rs9697457 0 934345 +1 rs6657048 0 957640 +1 rs2488991 0 994391 +1 rs307354 0 1264539 +1 rs1240719 0 1346905 +2 rs2862633 0 61974443 +2 rs28569024 0 139008811 +2 rs10106770 0 235832763 +3 rs11942835 0 155913651 +23 rs5945676 0 51433071 diff --git a/inst/extdata/pop_a_ped_plink.ped b/inst/extdata/pop_a_ped_plink.ped new file mode 100644 index 00000000..a48c2989 --- /dev/null +++ b/inst/extdata/pop_a_ped_plink.ped @@ -0,0 +1,5 @@ +pop_a GRC14300079 0 0 1 -9 A A A A G G A A G G T G G G C C T T C C T T G G T T A G T T T T +pop_a GRC14300142 0 0 1 -9 A A A A G G A A G G G G G G C C T T G C A T G G T T G G C T T T +pop_a GRC14300159 0 0 1 -9 A A G A A G A A A A T G G G C C T T C C T T G G T T A G T T T T +pop_a GRC14300286 0 0 1 -9 A A A A G G A A G G G G G G C C T T G C T T G G T T A G C T T T +pop_a GRC14300305 0 0 1 -9 A A A A A G A A A G T T G G C C T T C C T T G G T T A G T T T T diff --git a/inst/extdata/pop_a_ped_tidypopgen.map b/inst/extdata/pop_a_ped_tidypopgen.map new file mode 100644 index 00000000..dbe5526e --- /dev/null +++ b/inst/extdata/pop_a_ped_tidypopgen.map @@ -0,0 +1,16 @@ +1 rs4477212 0 82154 +1 rs3094315 0 752566 +1 rs3131972 0 752721 +1 rs12124819 0 776546 +1 rs11240777 0 798959 +1 rs1110052 0 873558 +1 rs9697457 0 934345 +1 rs6657048 0 957640 +1 rs2488991 0 994391 +1 rs307354 0 1264539 +1 rs1240719 0 1346905 +2 rs2862633 0 61974443 +2 rs28569024 0 139008811 +2 rs10106770 0 235832763 +3 rs11942835 0 155913651 +23 rs5945676 0 51433071 diff --git a/inst/extdata/pop_a_ped_tidypopgen.ped b/inst/extdata/pop_a_ped_tidypopgen.ped new file mode 100644 index 00000000..54d6586e --- /dev/null +++ b/inst/extdata/pop_a_ped_tidypopgen.ped @@ -0,0 +1,5 @@ +pop_a GRC14300079 0 0 0 -9 A A A A G G A A G G G T G G C C T T C C T T G G T T G A T T T T +pop_a GRC14300142 0 0 0 -9 A A A A G G A A G G G G G G C C T T C G T A G G T T G G T C T T +pop_a GRC14300159 0 0 0 -9 A A A G G A A A A A G T G G C C T T C C T T G G T T G A T T T T +pop_a GRC14300286 0 0 0 -9 A A A A G G A A G G G G G G C C T T C G T T G G T T G A T C T T +pop_a GRC14300305 0 0 0 -9 A A A A G A A A G A T T G G C C T T C C T T G G T T G A T T T T