Merge pull request #18 from HannahVMeyer/dev

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meyer-lab-cshl · Sep 25, 2019 · a875b9f · a875b9f
2 parents e8934e0 + e2a0fc8
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -15,3 +15,4 @@ inst/extdata/createData
 inst/extdata/plink_log
 pkgdown/
 ^cran-comments\.md$
+pkgdown/
diff --git a/NEWS.md b/NEWS.md
@@ -20,6 +20,8 @@
   containing only related individuals; fixes #11
 * Fix command for genotype conversion in 1000Genomes vignette, addressing issue
   #10
+* fix missing rownames error for overviewPerIndividualQC, when relatedness check
+  was included (issue #16, fc7a38b1f2b345d9c6c5d69f5dcf0bc57a857f62)
 
 
 # plinkQC 0.2.2

diff --git a/docs/articles/checkAncestry.png b/docs/articles/checkAncestry.png
diff --git a/docs/articles/checkHetImiss.png b/docs/articles/checkHetImiss.png
diff --git a/docs/articles/checkRelatedness.png b/docs/articles/checkRelatedness.png
diff --git a/docs/articles/checkSex.png b/docs/articles/checkSex.png
diff --git a/docs/articles/hwe.png b/docs/articles/hwe.png
diff --git a/docs/articles/individualQC.png b/docs/articles/individualQC.png
diff --git a/docs/articles/maf.png b/docs/articles/maf.png
diff --git a/docs/articles/markerQC.png b/docs/articles/markerQC.png
diff --git a/docs/articles/overviewQC.png b/docs/articles/overviewQC.png
diff --git a/docs/articles/plinkQC.html b/docs/articles/plinkQC.html
diff --git a/docs/articles/snpmissingness.png b/docs/articles/snpmissingness.png
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/relatednessFilter.html b/docs/reference/relatednessFilter.html
diff --git a/vignettes/checkAncestry.png b/vignettes/checkAncestry.png
diff --git a/vignettes/checkHetImiss.png b/vignettes/checkHetImiss.png
diff --git a/vignettes/checkRelatedness.png b/vignettes/checkRelatedness.png
diff --git a/vignettes/checkSex.png b/vignettes/checkSex.png
diff --git a/vignettes/hwe.png b/vignettes/hwe.png
diff --git a/vignettes/individualQC.pdf b/vignettes/individualQC.pdf
diff --git a/vignettes/individualQC.png b/vignettes/individualQC.png
diff --git a/vignettes/maf.png b/vignettes/maf.png
diff --git a/vignettes/markerQC.png b/vignettes/markerQC.png
diff --git a/vignettes/overviewQC.png b/vignettes/overviewQC.png
diff --git a/vignettes/checkAncestry.pdf → vignettes/pdf/checkAncestry.pdf b/vignettes/checkAncestry.pdf → vignettes/pdf/checkAncestry.pdf
diff --git a/vignettes/checkHetImiss.pdf → vignettes/pdf/checkHetImiss.pdf b/vignettes/checkHetImiss.pdf → vignettes/pdf/checkHetImiss.pdf
diff --git a/vignettes/checkRelatedness.pdf → vignettes/pdf/checkRelatedness.pdf b/vignettes/checkRelatedness.pdf → vignettes/pdf/checkRelatedness.pdf
diff --git a/vignettes/checkSex.pdf → vignettes/pdf/checkSex.pdf b/vignettes/checkSex.pdf → vignettes/pdf/checkSex.pdf
diff --git a/vignettes/hwe.pdf → vignettes/pdf/hwe.pdf b/vignettes/hwe.pdf → vignettes/pdf/hwe.pdf
diff --git a/vignettes/pdf/individualQC.pdf b/vignettes/pdf/individualQC.pdf
diff --git a/vignettes/maf.pdf → vignettes/pdf/maf.pdf b/vignettes/maf.pdf → vignettes/pdf/maf.pdf
diff --git a/vignettes/markerQC.pdf → vignettes/pdf/markerQC.pdf b/vignettes/markerQC.pdf → vignettes/pdf/markerQC.pdf
diff --git a/vignettes/overviewAncestryQC.pdf → vignettes/pdf/overviewAncestryQC.pdf b/vignettes/overviewAncestryQC.pdf → vignettes/pdf/overviewAncestryQC.pdf
diff --git a/vignettes/overviewMarkerQC.pdf → vignettes/pdf/overviewMarkerQC.pdf b/vignettes/overviewMarkerQC.pdf → vignettes/pdf/overviewMarkerQC.pdf
diff --git a/vignettes/overviewQC.pdf → vignettes/pdf/overviewQC.pdf b/vignettes/overviewQC.pdf → vignettes/pdf/overviewQC.pdf
diff --git a/vignettes/snpmissingness.pdf → vignettes/pdf/snpmissingness.pdf b/vignettes/snpmissingness.pdf → vignettes/pdf/snpmissingness.pdf
diff --git a/vignettes/plinkQC.Rmd b/vignettes/plinkQC.Rmd
@@ -115,6 +115,10 @@ individual IDs to the qcdir. These IDs will be removed in the computation of the
 `perMarkerQC`. If the list is not present, `perMarkerQC` will send a message
 about conducting the quality control on the entire dataset.
 
+NB: To reduce the data size of the example data in `plinkQC`,
+data.genome  has already been reduced to the individuals that are related. Thus
+the relatedness plots in C only show counts for related individuals only.
+
 NB: To demonstrate the results of the ancestry check, the required eigenvector
 file of the combined study and reference datasets have been precomputed and
 for the purpose of this example will be copied to the `qcdir`. In practice,
@@ -156,7 +160,6 @@ overview_individuals <- overviewPerIndividualQC(fail_individuals,
 ```{r load overviewIndividualQC, out.width = "500px", echo=FALSE}
 par(mfrow=c(2,1), las=1)
 knitr::include_graphics("overviewQC.png")
-knitr::include_graphics("overviewAncestryQC.png")
 ```
 
 
@@ -273,6 +276,10 @@ complex family structures, the unrelated individuals per family are selected
 (e.g. in a parents-offspring trio, the offspring will be marked as fail, while 
 the parents will be kept in the analysis).
 
+NB: To reduce the data size of the example data in `plinkQC`,
+data.genome  has already been reduced to the individuals that are related. Thus
+the relatedness plots in C only show counts for related individuals only.
+
 ```{r check related, eval=FALSE, fig.height=3, fig.width=5, fig.align='center'}
 exclude_relatedness <- check_relatedness(indir=indir, qcdir=qcdir, name=name,
                                          interactive=TRUE,

diff --git a/vignettes/snpmissingness.png b/vignettes/snpmissingness.png