From 625bb9771d076d978265a16b16b989debcc4334d Mon Sep 17 00:00:00 2001 From: Christian Huber Date: Wed, 23 Jun 2021 10:30:32 -0400 Subject: [PATCH] Fix vignette --- .DS_Store | Bin 8196 -> 8196 bytes .../Converting_VCF_and_PLINK_formats.html | 2 +- docs/pkgdown.yml | 2 +- .../Converting_VCF_and_PLINK_formats.Rmd | 2 +- .../Converting_VCF_and_PLINK_formats.Rmd.orig | 2 +- 5 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.DS_Store b/.DS_Store index 2923b76ebcd1a1af6557be998b6b2b7fc9354ff2..81ea77bf8821db6ceaebf84e4ae4f06a593a1ff6 100644 GIT binary patch delta 37 tcmZp1XmOa}&&ahgU^hP_*Jd689>&d*Lho2NHZU@7W|#QRvaynl835Sz3n>5q delta 70 zcmZp1XmOa}&&abeU^hP_&t@J09!6d^hBSsuhIEEfh9ZX4$%=yglc$P!qKa

PLINK to raw genotype (.traw)

-

Now we will use the plink2 software to transform the .bed file into raw genotypes. Again, note that we will need a “transformed” version since smartsnp assumes that samples are in columns, not rows.

+

Now we will use the plink2 software to transform the .bed file into raw genotypes. Again, note that we will need a “transposed” version since smartsnp assumes that samples are in columns, not rows.

 system("plink --bfile region --recode A-transpose --out region_genotypeMatrix")

Again, the –out parameter defines the name of the output file, without the suffix. After running this command, you will see a “region_genotypeMatrix.traw” file. This file can be directly used with smartsnp.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index bc3e270..92820c0 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,5 +5,5 @@ articles: Converting_VCF_and_PLINK_formats: Converting_VCF_and_PLINK_formats.html aDNA_smartpca_analysis: aDNA_smartpca_analysis.html mallard_smartpca_analysis: mallard_smartpca_analysis.html -last_built: 2021-06-21T15:19Z +last_built: 2021-06-23T14:29Z diff --git a/vignettes/Converting_VCF_and_PLINK_formats.Rmd b/vignettes/Converting_VCF_and_PLINK_formats.Rmd index b8e48ef..1b76022 100644 --- a/vignettes/Converting_VCF_and_PLINK_formats.Rmd +++ b/vignettes/Converting_VCF_and_PLINK_formats.Rmd @@ -72,7 +72,7 @@ If you don't want to make use of any further *plink2* functionality, then you ca ## PLINK to raw genotype (.traw) -Now we will use the *plink2* software to transform the .bed file into raw genotypes. Again, note that we will need a "transformed" version since *smartsnp* assumes that samples are in columns, not rows. +Now we will use the *plink2* software to transform the .bed file into raw genotypes. Again, note that we will need a "transposed" version since *smartsnp* assumes that samples are in columns, not rows. ```r diff --git a/vignettes/Converting_VCF_and_PLINK_formats.Rmd.orig b/vignettes/Converting_VCF_and_PLINK_formats.Rmd.orig index ef00f27..813302f 100644 --- a/vignettes/Converting_VCF_and_PLINK_formats.Rmd.orig +++ b/vignettes/Converting_VCF_and_PLINK_formats.Rmd.orig @@ -73,7 +73,7 @@ If you don't want to make use of any further *plink2* functionality, then you ca ## PLINK to raw genotype (.traw) -Now we will use the *plink2* software to transform the .bed file into raw genotypes. Again, note that we will need a "transformed" version since *smartsnp* assumes that samples are in columns, not rows. +Now we will use the *plink2* software to transform the .bed file into raw genotypes. Again, note that we will need a "transposed" version since *smartsnp* assumes that samples are in columns, not rows. ```{r} system("plink --bfile region --recode A-transpose --out region_genotypeMatrix")