Include explicit reference to ancestry estimation vignette

meyer-lab-cshl · Feb 3, 2021 · 416f9fe · 416f9fe
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diff --git a/vignettes/Genomes1000.Rmd b/vignettes/Genomes1000.Rmd
@@ -36,7 +36,8 @@ The following vignette shows the processing steps required to use samples of the
 1000 Genomes study [@a1000Genomes2015],[@b1000Genomes2015] as a reference
 dataset. Using the 1000 Genomes reference, population structure down to
 large-scale continental ancestry can be detected. A step-by-step instruction on
-how to conduct this ancestry analysis is described in this [vignette](https://meyer-lab-cshl.github.io/plinkQC/articles/AncestryCheck.html).
+how to conduct this ancestry analysis is described in this
+[Ancestry estimation vignette](https://meyer-lab-cshl.github.io/plinkQC/articles/AncestryCheck.html).
 
 
 # Workflow
@@ -111,4 +112,10 @@ plink2 --pfile $refdir/all_phase3 vzs\
 mv $refdir/all_phase3.log $refdir/log
 ```
 
+
+After these steps, the 1000 Genomes dataset can be used 
+for inferring study ancestry as described in the corresponding
+[Ancestry estimation vignette](https://meyer-lab-cshl.github.io/plinkQC/articles/AncestryCheck.html).
+
 # References
+
diff --git a/vignettes/HapMap.Rmd b/vignettes/HapMap.Rmd
@@ -36,7 +36,8 @@ The following vignette shows the processing steps required to use samples of the
 HapMap study [@HapMap2005][@HapMap2007][@HapMap2010] as a reference dataset. 
 Using this reference, population structure down to large-scale continental
 ancestry can be detected. A step-by-step instruction on how to conduct this
-analysis is described in this [vignette](https://meyer-lab-cshl.github.io/plinkQC/articles/AncestryCheck.html).
+analysis is described in this
+[Ancestry estimation vignette](https://meyer-lab-cshl.github.io/plinkQC/articles/AncestryCheck.html).
 
 
 # Workflow
@@ -143,7 +144,7 @@ awk '{print $4, $3}' $refdir/HapMapIII_CGRCh37 > $refdir/HapMapIII_CGRCh37.pos
 ## Update the reference data
 We can now use PLINK to extract the mappable variants from the old build and
 update their position. After these steps, the HapMap III dataset can be used 
-for inferring study ancestry as described in the corresponding [vignette](https://meyer-lab-cshl.github.io/plinkQC/articles/AncestryCheck.html).
+for inferring study ancestry as described in the corresponding [Ancestry estimation vignette](https://meyer-lab-cshl.github.io/plinkQC/articles/AncestryCheck.html).
 ```{bash update annotation, eval=FALSE}
 plink --bfile $refdir/HapMapIII_NCBI36 \
     --extract $refdir/HapMapIII_CGRCh37.snps \