vignettes/Intro_qsvaR.Rmd
Intro_qsvaR.RmdqsvaR#> Stolz JM, Tnani H, Collado-Torres L (2023). _qsvaR_.
#> doi:10.18129/B9.bioc.qsvaR <https://doi.org/10.18129/B9.bioc.qsvaR>,
#> https://github.com/LieberInstitute/qsvaR/qsvaR - R package version
-#> 1.5.2, <http://www.bioconductor.org/packages/qsvaR>.
+#> 1.5.3, <http://www.bioconductor.org/packages/qsvaR>.
#>
#> Stolz JM, Tnani H, Tao R, Jaffe AE, Collado-Torres L (2023). "qsvaR."
#> _bioRxiv_. doi:10.1101/TODO <https://doi.org/10.1101/TODO>,
@@ -610,9 +610,9 @@ Date the vignette was generated.
-#> [1] "2023-06-21 21:35:33 UTC"#> [1] "2023-06-27 14:22:20 UTC"Wallclock time spent generating the vignette.
-#> Time difference of 1.397 mins#> Time difference of 1.653 minsR session information.
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
#> setting value
@@ -624,7 +624,7 @@ Reproducibility#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz UTC
-#> date 2023-06-21
+#> date 2023-06-27
#> pandoc 2.19.2 @ /usr/local/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -667,7 +667,7 @@ Reproducibility#> fs 1.6.2 2023-04-25 [2] RSPM (R 4.3.0)
#> genefilter 1.82.1 2023-05-02 [1] Bioconductor
#> generics 0.1.3 2022-07-05 [1] RSPM (R 4.3.0)
-#> GenomeInfoDb * 1.36.0 2023-04-25 [1] Bioconductor
+#> GenomeInfoDb * 1.36.1 2023-06-21 [1] Bioconductor
#> GenomeInfoDbData 1.2.10 2023-05-17 [1] Bioconductor
#> GenomicRanges * 1.52.0 2023-04-25 [1] Bioconductor
#> ggplot2 3.4.2 2023-04-03 [1] RSPM (R 4.3.0)
@@ -676,7 +676,7 @@ Reproducibility#> highr 0.10 2022-12-22 [2] RSPM (R 4.3.0)
#> htmltools 0.5.5 2023-03-23 [2] RSPM (R 4.3.0)
#> httr 1.4.6 2023-05-08 [2] RSPM (R 4.3.0)
-#> IRanges * 2.34.0 2023-04-25 [1] Bioconductor
+#> IRanges * 2.34.1 2023-06-22 [1] Bioconductor
#> jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.3.0)
#> jsonlite 1.8.5 2023-06-05 [2] RSPM (R 4.3.0)
#> KEGGREST 1.40.0 2023-04-25 [1] Bioconductor
@@ -701,7 +701,7 @@ Reproducibility#> plyr 1.8.8 2022-11-11 [1] RSPM (R 4.3.0)
#> png 0.1-8 2022-11-29 [1] RSPM (R 4.3.0)
#> purrr 1.0.1 2023-01-10 [2] RSPM (R 4.3.0)
-#> qsvaR * 1.5.2 2023-06-21 [1] Bioconductor
+#> qsvaR * 1.5.3 2023-06-27 [1] Bioconductor
#> R6 2.5.1 2021-08-19 [2] RSPM (R 4.3.0)
#> ragg 1.2.5 2023-01-12 [2] RSPM (R 4.3.0)
#> Rcpp 1.0.10 2023-01-22 [2] RSPM (R 4.3.0)
@@ -820,7 +820,7 @@ Bibliography[10]
J. M. Stolz, H. Tnani, and L. Collado-Torres. qsvaR. https://github.com/LieberInstitute/qsvaR/qsvaR - R
-package version 1.5.2. 2023. DOI:
+package version 1.5.3. 2023. DOI:
10.18129/B9.bioc.qsvaR.
URL:
http://www.bioconductor.org/packages/qsvaR.
diff --git a/articles/index.html b/articles/index.html
index dcded30..8397043 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
diff --git a/authors.html b/authors.html
index bdb45ef..243711b 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
@@ -81,14 +81,14 @@ Citation
Stolz JM, Tnani H, Collado-Torres L (2023).
qsvaR.
-doi:10.18129/B9.bioc.qsvaR, https://github.com/LieberInstitute/qsvaR/qsvaR - R package version 1.5.2, http://www.bioconductor.org/packages/qsvaR.
+doi:10.18129/B9.bioc.qsvaR, https://github.com/LieberInstitute/qsvaR/qsvaR - R package version 1.5.3, http://www.bioconductor.org/packages/qsvaR.
@Manual{,
title = {qsvaR},
author = {Joshua M. Stolz and Hedia Tnani and Leonardo Collado-Torres},
year = {2023},
url = {http://www.bioconductor.org/packages/qsvaR},
- note = {https://github.com/LieberInstitute/qsvaR/qsvaR - R package version 1.5.2},
+ note = {https://github.com/LieberInstitute/qsvaR/qsvaR - R package version 1.5.3},
doi = {10.18129/B9.bioc.qsvaR},
}
Stolz JM, Tnani H, Tao R, Jaffe AE, Collado-Torres L (2023).
diff --git a/index.html b/index.html
index 604d929..c5f2b71 100644
--- a/index.html
+++ b/index.html
@@ -38,7 +38,7 @@
diff --git a/news/index.html b/news/index.html
index d8d45ca..612ea74 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
@@ -57,6 +57,12 @@
Changelog
Source: NEWS.md
+
+qsvaR 1.5.3
+BUG FIXES
+- Fixed the error messages displayed by
k_qsvs() to handle different types of situations. We implemented this update with @HediaTnani, @reneegf, and
+
-
+
qsvaR 1.5.2
BUG FIXES
diff --git a/pkgdown.yml b/pkgdown.yml
index 2fa4fe8..4226c59 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
pkgdown_sha: ~
articles:
Intro_qsvaR: Intro_qsvaR.html
-last_built: 2023-06-21T21:33Z
+last_built: 2023-06-27T14:20Z
diff --git a/reference/DEqual.html b/reference/DEqual.html
index 43fc852..06cb801 100644
--- a/reference/DEqual.html
+++ b/reference/DEqual.html
@@ -25,7 +25,7 @@
diff --git a/reference/covComb_tx_deg.html b/reference/covComb_tx_deg.html
index e2ecb20..e181d12 100644
--- a/reference/covComb_tx_deg.html
+++ b/reference/covComb_tx_deg.html
@@ -20,7 +20,7 @@
diff --git a/reference/degradation_tstats.html b/reference/degradation_tstats.html
index c5ae972..b24aac0 100644
--- a/reference/degradation_tstats.html
+++ b/reference/degradation_tstats.html
@@ -21,7 +21,7 @@
diff --git a/reference/getDegTx.html b/reference/getDegTx.html
index 67deeee..877949e 100644
--- a/reference/getDegTx.html
+++ b/reference/getDegTx.html
@@ -20,7 +20,7 @@
diff --git a/reference/getPCs.html b/reference/getPCs.html
index 13514cc..903d656 100644
--- a/reference/getPCs.html
+++ b/reference/getPCs.html
@@ -17,7 +17,7 @@
diff --git a/reference/get_qsvs.html b/reference/get_qsvs.html
index 454e6c5..500ebf8 100644
--- a/reference/get_qsvs.html
+++ b/reference/get_qsvs.html
@@ -18,7 +18,7 @@
diff --git a/reference/index.html b/reference/index.html
index 4c690ad..9f2b62e 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
diff --git a/reference/k_qsvs.html b/reference/k_qsvs.html
index 6a76f64..de4f096 100644
--- a/reference/k_qsvs.html
+++ b/reference/k_qsvs.html
@@ -17,7 +17,7 @@
diff --git a/reference/qSVA.html b/reference/qSVA.html
index 1546d8f..b673e76 100644
--- a/reference/qSVA.html
+++ b/reference/qSVA.html
@@ -17,7 +17,7 @@
diff --git a/reference/select_transcripts.html b/reference/select_transcripts.html
index 511c740..c67317d 100644
--- a/reference/select_transcripts.html
+++ b/reference/select_transcripts.html
@@ -17,7 +17,7 @@
diff --git a/reference/transcripts.html b/reference/transcripts.html
index 7960ac0..2c6b88f 100644
--- a/reference/transcripts.html
+++ b/reference/transcripts.html
@@ -22,7 +22,7 @@