Merge branch 'master' of git.bioconductor.org:packages/MAST into master

.travis.yml

@@ -1,8 +1,5 @@
 # Sample .travis.yml for R projects
-
 language: r
-r: bioc-devel
-dist: trusty
 sudo: required
 
 matrix:
@@ -12,44 +9,60 @@ matrix:
    - os: linux
      r: devel
      env: R_CODECOV=true
-
-r_binary_packages: 
+
+cache: 
+  packages: TRUE
+
+before_install:
+  - R -e 'install.packages("devtools")'
+  - tlmgr install index
+  - sudo apt-get update
+  - sudo apt-get -y install libharfbuzz-dev libfribidi-dev
+
+r_packages:
+  - data.table
+  - shiny
+  - shinythemes
+  - MASS
+  - methods
+  - stats
+  - utils
+  - graphics
+  - grDevices
+  - tools
+  - magrittr
+  - rmarkdown
+  - robustbase
+  - ggplot2
   - BiocStyle
   - lme4
   - GGally
-  - ggplot2
   - reshape2
-  - data.table
-  - knitr
   - stringr
   - NMF
   - rsvd
   - RColorBrewer
 
-before_install:
-  - R -e 'install.packages("devtools")'
-  - tlmgr install index
-
-install:
-  - R -e 'devtools::install_deps(dep = T,type="source")'
+r_github_packages:
+  - jrowen/rhandsontable
+  - rlbarter/superheat
+  - yihui/knitr
+  - r-lib/covr
+  - r-lib/testthat
+  - r-lib/vdiffr
+  - r-lib/pkgdown
+  - rstudio/shinytest
+
+use_bioc: true
 
 bioc_packages:
+  - BiocGenerics
   - GSEABase
   - limma
   - TxDb.Hsapiens.UCSC.hg19.knownGene
 
-cache: 
-  packages: TRUE
-
-warnings_are_errors: false 
-
-use_bioc: true
-
-bioc_required: true
 
-env:
- global:
-   - CRAN: http://cran.rstudio.com
+warnings_are_errors: false
 
 notifications:
   email:
@@ -58,5 +71,16 @@ notifications:
 
 after_success:
   -  if [[ "${R_CODECOV}" ]]; then R -e 'covr::codecov()'; fi
-
+
+env:
+ global:
+   - CRAN: http://cran.rstudio.com
+   - BIOC_USE_DEVEL="FALSE"
+
+
+
+
+
+
+
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: MAST
 Type: Package
 Title: Model-based Analysis of Single Cell Transcriptomics
-Version: 1.15.0
+Version: 1.17.1
 Date: 2020-03-21
 Authors@R: c(person("Andrew", "McDavid", email = "[email protected]", role = c("aut", "cre")),
             person("Greg", "Finak", email="[email protected]", role='aut'),
@@ -88,7 +88,7 @@ Collate:
     'thresholdSCRNA.R'
     'zeroinf.R'
     'zlmHooks.R'
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 LazyData: true
 biocViews: GeneExpression, DifferentialExpression, GeneSetEnrichment,
     RNASeq, Transcriptomics, SingleCell

R/ZlmFit.R

@@ -1,8 +1,11 @@
 Glue <- function(...) abind(..., rev.along=0)
 
+#'@importFrom plyr rbind.fill
 collectSummaries <- function(listOfSummaries){
     summaries <- list()
-    summaries[['coefC']] <- do.call(rbind, lapply(listOfSummaries, '[[', 'coefC'))
+    #summaries[['coefC']] <- do.call(rbind, lapply(listOfSummaries, '[[', 'coefC'))
+    summaries[['coefC']] <- as.matrix(do.call(plyr::rbind.fill,lapply(lapply(listOfSummaries,"[[", "coefC"),function(x)as.data.frame(t(x)))))
+    rownames(summaries[['coefC']])<-names(listOfSummaries)
     summaries[['vcovC']] <- do.call(Glue, lapply(listOfSummaries, '[[', 'vcovC'))
     summaries[['df.resid']] <- do.call(rbind, lapply(listOfSummaries, '[[', 'df.resid'))
     summaries[['df.null']] <- do.call(rbind, lapply(listOfSummaries, '[[', 'df.null'))
@@ -11,8 +14,11 @@ collectSummaries <- function(listOfSummaries){
     summaries[['dispersionNoshrink']] <- do.call(rbind, lapply(listOfSummaries, '[[', 'dispersionNoshrink'))
     summaries[['converged']] <- do.call(rbind, lapply(listOfSummaries, '[[', 'converged'))
     summaries[['loglik']] <- do.call(rbind, lapply(listOfSummaries, '[[', 'loglik'))
-    summaries[['coefD']] <- do.call(rbind, lapply(listOfSummaries, '[[', 'coefD'))
+    #summaries[['coefD']] <- do.call(rbind, lapply(listOfSummaries, '[[', 'coefD'))
     summaries[['vcovD']] <- do.call(Glue, lapply(listOfSummaries, '[[', 'vcovD'))
+    summaries[['coefD']] <-as.matrix(do.call(plyr::rbind.fill,lapply(lapply(listOfSummaries,"[[", "coefD"),function(x)as.data.frame(t(x)))))
+    rownames(summaries[['coefD']])<-names(listOfSummaries)
+
 
     summaries
 }