From 94899d11b0e000cc04f4c0f7f98728a39de9bc20 Mon Sep 17 00:00:00 2001 From: Martin Petr Date: Sun, 2 Dec 2018 23:25:45 +0100 Subject: [PATCH] Incrementing version number --- DESCRIPTION | 2 +- NEWS.md | 5 +++++ docs/LICENSE-text.html | 2 +- docs/LICENSE.html | 2 +- docs/articles/index.html | 2 +- docs/articles/tutorial.html | 24 ++++++++++++------------ docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 10 +++++++++- docs/reference/count_snps.html | 2 +- docs/reference/download_data.html | 2 +- docs/reference/eigenstrat.html | 2 +- docs/reference/f4ratio.html | 2 +- docs/reference/filter_bed.html | 2 +- docs/reference/index.html | 2 +- docs/reference/merge_eigenstrat.html | 2 +- docs/reference/pipe.html | 2 +- docs/reference/print.EIGENSTRAT.html | 2 +- docs/reference/qpAdm.html | 2 +- docs/reference/qpWave.html | 2 +- docs/reference/read_ind.html | 2 +- docs/reference/relabel.html | 2 +- docs/reference/reset.html | 2 +- docs/reference/write_ind.html | 2 +- 24 files changed, 47 insertions(+), 34 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 48f9d5b..ffc88d9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: admixr Title: An Interface for Running ADMIXTOOLS Analyses Directly from R -Version: 0.7.0 +Version: 0.7.1 Authors@R: person("Martin", "Petr", email = "mp@bodkan.net", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4879-8421")) Description: A convenient interface for performing all stages of ADMIXTOOLS diff --git a/NEWS.md b/NEWS.md index 0ca23a6..c6545e5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# admixr 0.7.1 + +* Parse admixture proportions from the "best coefficients" line of the qpAdm + output file. + # admixr 0.7.0 * Fixed handling of warnings when dealing with duplicated populations. diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 150253b..5d61f4c 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -58,7 +58,7 @@ admixr - 0.7.0 + 0.7.1 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 88474a8..34e4dd2 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -58,7 +58,7 @@ admixr - 0.7.0 + 0.7.1 diff --git a/docs/articles/index.html b/docs/articles/index.html index c15609c..7de4698 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -58,7 +58,7 @@ admixr - 0.7.0 + 0.7.1 diff --git a/docs/articles/tutorial.html b/docs/articles/tutorial.html index 9249456..8776b9a 100644 --- a/docs/articles/tutorial.html +++ b/docs/articles/tutorial.html @@ -29,7 +29,7 @@ admixr - 0.7.0 + 0.7.1 @@ -145,12 +145,12 @@

Therefore, a VCF file is essentially a combination of all three files in a single package. Luckily for us, all three EIGENSTRAT files usually share a common path and prefix and should be placed in a single directory.

Let’s first download a small testing SNP dataset using a built-in admixr function download_data(). This function downloads the data into a temporary directory (you can specify the destination using its dirname argument). In addition to this, the function returns a shared prefix of the whole dataset.

+[1] "/var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps"

We can verify that there are indeed three files with this prefix:

+[1] "/var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps.geno" +[2] "/var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps.ind" +[3] "/var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps.snp"

Let’s look at their contents:

+#> ind file: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps.ind +#> snp file: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps.snp +#> geno file: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps.geno

This object simply encapsulates the paths to all three EIGENSTRAT components and makes it easy to pass the data to different admixr functions.

The following couple of sections describe how to use the admixr package on a set of example analyses.

@@ -1037,12 +1037,12 @@

#> EIGENSTRAT object #> ================= #> components: -#> ind file: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//RtmpkO1AZM/snps/snps.ind -#> snp file: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//RtmpkO1AZM/snps/snps.snp -#> geno file: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//RtmpkO1AZM/snps/snps.geno +#> ind file: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps.ind +#> snp file: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps.snp +#> geno file: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/snps/snps.geno #> #> modifiers: -#> groups: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//RtmpkO1AZM/file4fc351adae1d.ind +#> groups: /var/folders/kk/s4cwdkx90pscz314mp0hhz480000gn/T//Rtmpiusthx/file5d946113abb5.ind

We can see that the function relabel returned a modified EIGENSTRAT object, which contains a new item in the “modifiers” section - the path to a new ind file that will be used in downstream analyses. Let’s look at its contents:

Chimp        U  Chimp
 Mbuti        U  African
diff --git a/docs/authors.html b/docs/authors.html
index 1e337b8..7df62c0 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -58,7 +58,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/index.html b/docs/index.html
index cac40fb..dd536a2 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -36,7 +36,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 722c71f..28e05f3 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -58,7 +58,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
@@ -113,6 +113,13 @@ 
Changelog 

       Source: NEWS.md
     
 
+    

+

+admixr 0.7.1

+
    
+
  • Parse admixture proportions from the “best coefficients” line of the qpAdm output file.
    • 
+

+

     

 

 admixr 0.7.0

@@ -221,6 +228,7 @@ 

     

       
Contents

       
    
+        
  • 0.7.1
    • 
         
  • 0.7.0
    • 
         
  • 0.6.3
    • 
         
  • 0.6.2
    • 
diff --git a/docs/reference/count_snps.html b/docs/reference/count_snps.html
index b95a82f..3ef48dc 100644
--- a/docs/reference/count_snps.html
+++ b/docs/reference/count_snps.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     

 
diff --git a/docs/reference/download_data.html b/docs/reference/download_data.html
index d9407fc..8e96197 100644
--- a/docs/reference/download_data.html
+++ b/docs/reference/download_data.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     

 
diff --git a/docs/reference/eigenstrat.html b/docs/reference/eigenstrat.html
index 0131cea..1007dd4 100644
--- a/docs/reference/eigenstrat.html
+++ b/docs/reference/eigenstrat.html
@@ -62,7 +62,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/f4ratio.html b/docs/reference/f4ratio.html
index 9c7fd01..366e76e 100644
--- a/docs/reference/f4ratio.html
+++ b/docs/reference/f4ratio.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/filter_bed.html b/docs/reference/filter_bed.html
index 8e697f5..9d4ea47 100644
--- a/docs/reference/filter_bed.html
+++ b/docs/reference/filter_bed.html
@@ -62,7 +62,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 80d89ee..616e38e 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,7 +58,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/merge_eigenstrat.html b/docs/reference/merge_eigenstrat.html
index d9dc0e8..db3716d 100644
--- a/docs/reference/merge_eigenstrat.html
+++ b/docs/reference/merge_eigenstrat.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html
index fd410a6..2816686 100644
--- a/docs/reference/pipe.html
+++ b/docs/reference/pipe.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/print.EIGENSTRAT.html b/docs/reference/print.EIGENSTRAT.html
index f2b5f1c..430d3b5 100644
--- a/docs/reference/print.EIGENSTRAT.html
+++ b/docs/reference/print.EIGENSTRAT.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/qpAdm.html b/docs/reference/qpAdm.html
index c18ffaf..9de71cd 100644
--- a/docs/reference/qpAdm.html
+++ b/docs/reference/qpAdm.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/qpWave.html b/docs/reference/qpWave.html
index b0e53bd..19c5f2b 100644
--- a/docs/reference/qpWave.html
+++ b/docs/reference/qpWave.html
@@ -62,7 +62,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/read_ind.html b/docs/reference/read_ind.html
index e22b21e..d83c31d 100644
--- a/docs/reference/read_ind.html
+++ b/docs/reference/read_ind.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/relabel.html b/docs/reference/relabel.html
index 3c11f8f..e26a234 100644
--- a/docs/reference/relabel.html
+++ b/docs/reference/relabel.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/reset.html b/docs/reference/reset.html
index d419676..8651e94 100644
--- a/docs/reference/reset.html
+++ b/docs/reference/reset.html
@@ -62,7 +62,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1
       
     
 
diff --git a/docs/reference/write_ind.html b/docs/reference/write_ind.html
index 129a012..2168a2c 100644
--- a/docs/reference/write_ind.html
+++ b/docs/reference/write_ind.html
@@ -61,7 +61,7 @@
       
       
         admixr
-        0.7.0
+        0.7.1