update from remote

.travis.yml

@@ -6,7 +6,7 @@ r:
 #  - release
 #  - bioc-release
 sudo: false
-#cache: packages
+cache: packages
 
 dist: xenial
 
@@ -18,7 +18,7 @@ addons:
     packages:
       - libgsl-dev # dependency for gsl>copula>zinbwave
       - libmagick++-dev # dependency for magick
-r_check_args: "--no-vignettes"
+#r_check_args: "--no-vignettes"
 
 install: skip
 #install:

DESCRIPTION

@@ -32,11 +32,10 @@ Imports:
     fitdistrplus,
     ggplot2,
     locfit,
-    data.table,
     matrixStats,
     methods,
     scales,
-    scater (>= 1.15.16),
+    scater, 
     stats,
     SummarizedExperiment,
     utils,
@@ -47,6 +46,7 @@ Suggests:
     BiocStyle,
     covr,
     cowplot,
+    knitr,
     magick,
     dplyr,
     limSolve,
@@ -71,5 +71,6 @@ biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
 URL: https://github.com/Oshlack/splatter
 BugReports: https://github.com/Oshlack/splatter/issues
 RoxygenNote: 7.0.2
+VignetteBuilder: knitr
 Encoding: UTF-8
 Language: en-GB

NAMESPACE

@@ -70,6 +70,7 @@ export(splatSimulate)
 export(splatSimulateGroups)
 export(splatSimulatePaths)
 export(splatSimulateSingle)
+export(splateQTL)
 export(summariseDiff)
 export(zinbEstimate)
 export(zinbSimulate)
@@ -149,6 +150,8 @@ importFrom(stats,ks.test)
 importFrom(stats,median)
 importFrom(stats,model.matrix)
 importFrom(stats,nls)
+importFrom(stats,pnorm)
+importFrom(stats,qgamma)
 importFrom(stats,rbinom)
 importFrom(stats,rchisq)
 importFrom(stats,rgamma)
@@ -159,3 +162,5 @@ importFrom(stats,rpois)
 importFrom(stats,runif)
 importFrom(stats,shapiro.test)
 importFrom(utils,head)
+importFrom(utils,read.delim)
+importFrom(utils,write.table)

man/splatSimulate.Rd

@@ -9,12 +9,8 @@
 \usage{
 splatSimulate(
   params = newSplatParams(),
-<<<<<<< HEAD
   method = c("single", "groups", "paths", "eqtl"),
-  eqtl = NaN,
-=======
-  method = c("single", "groups", "paths"),
->>>>>>> 083be7cc6b2b1aad391ab836b57bd0e565a022c3
+  eqtl = NULL,
   verbose = TRUE,
   ...
 )