Merge branch 'devel'

Former-commit-id: f54784f

.Rbuildignore

@@ -1,12 +1,16 @@
+^Meta$
+^doc$
 ^\.travis\.yml$
 ^R/\.wip
 ^docker
 ^run_tests
 ^\.
+^inferCNV\.wiki
 ^infercnv.Rdata
 ^inferCNV.Rproj
 ^Rstudio_helpers
 ^__simulations
+^example
 ^example/full_precision
 ^example/example.html
 ^example/test_subdir

.gitignore

@@ -1,3 +1,5 @@
+Meta
+doc
 .idea
 .Rproj.user
 .Rhistory

.travis.yml

@@ -1,3 +1,13 @@
 language: r
 r: bioc-release
 
+before_install:
+  - sudo apt-get update
+  - sudo apt-get install r-cran-rjags 
+
+# r_build_args: --no-build-vignettes --no-manual --no-resave-data
+r_check_args: --no-build-vignettes # --no-manual
+
+#script:
+#- travis_wait R CMD build .
+#- R CMD check --no-build-vignettes *tar.gz

DESCRIPTION

@@ -1,27 +1,38 @@
 Package: infercnv
 Type: Package
 Title: Infer Copy Number Variation from Single-Cell RNA-Seq Data
-Version: 0.8.2
+Version: 0.99.0
 Date: 2018-11-08
 Authors@R: c( person("Timothy", "Tickle", email = "ttickle@broadinstitute.org", role = c("aut", "cre")), person("Itay", "Tirosh", email = "tirosh@broadinstitute.org", role = "aut"), person("Christophe", "Georgescu", email = "cgeorges@broadinstitute.org", role = "aut"), person("Maxwell", "Brown", email = "mbrown@broadinstitute.org", role = "aut"), person("Brian", "Haas", email = "bhaas@broadinstitute.org", role = "aut")) 
 Author: Timothy Tickle [aut, cre], Itay Tirosh [aut], Christophe Georgescu [aut], Maxwell Brown [aut], Brian Haas [aut]
 Maintainer: Christophe Georgescu <cgeorges@broadinstitute.org>
 BugReports: https://github.com/broadinstitute/inferCNV/issues
 Description: Using single-cell RNA-Seq expression to visualize CNV in cells.
-Depends: R(>= 3.2.1)
+biocViews: Software, CopyNumberVariation, VariantDetection, StructuralVariation, GenomicVariation, Genetics, Transcriptomics, StatisticalMethod, Bayesian, HiddenMarkovModel, SingleCell
+Depends: R(>= 3.5)
 License: BSD_3_clause + file LICENSE
 LazyData: TRUE
 VignetteBuilder: knitr
 Suggests: BiocStyle, knitr, rmarkdown, testthat
-Enhances: NGCHM
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 NeedsCompilation: no
-Imports: RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, Matrix, binhf, fastcluster, dplyr, coin
+SystemRequirements: JAGS 4.x.y
+Imports: graphics, grDevices, RColorBrewer, gplots, futile.logger, stats, utils, methods, ape, Matrix,  fastcluster, dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, reshape, rjags, fitdistrplus, future, foreach, doParallel, BiocGenerics, SummarizedExperiment, SingleCellExperiment, tidyr, parallel, coda, gridExtra, argparse
+BugReports: https://github.com/broadinstitute/inferCNV/issues
+URL: https://github.com/broadinstitute/inferCNV/wiki
 Collate: 
-    'NextGenHeatMap.R'
+    'SplatterScrape.R'
     'inferCNV.R'
+    'inferCNV_BayesNet.R'
+    'inferCNV_HMM.R'
     'inferCNV_constants.R'
     'inferCNV_heatmap.R'
+    'inferCNV_hidden_spike.R'
+    'inferCNV_i3HMM.R'
     'inferCNV_mask_non_DE.R'
+    'inferCNV_meanVarSim.R'
     'inferCNV_ops.R'
-    'inferCNV_spike.R'
+    'inferCNV_simple_sim.R'
+    'inferCNV_tumor_subclusters.R'
+    'inferCNV_tumor_subclusters.random_smoothed_trees.R'
+    'noise_reduction.R'

NAMESPACE

@@ -1,49 +1,100 @@
 # Generated by roxygen2: do not edit by hand
 
+export(.i3HMM_get_sd_trend_by_num_cells_fit)
 export(CreateInfercnvObject)
 export(anscombe_transform)
 export(apply_max_threshold_bounds)
+export(apply_median_filtering)
+export(assign_HMM_states_to_proxy_expr_vals)
 export(center_cell_expr_across_chromosome)
 export(clear_noise)
 export(clear_noise_via_ref_mean_sd)
-export(compute_normalization_factor)
+export(determine_mean_delta_via_Z)
+export(filterHighPNormals)
+export(generate_cnv_region_reports)
 export(get_DE_genes_basic)
 export(get_average_bounds)
+export(get_hspike_cnv_mean_sd_trend_by_num_cells_fit)
+export(get_predicted_CNV_regions)
 export(get_reference_grouped_cell_indices)
+export(get_spike_dists)
+export(i3HMM_assign_HMM_states_to_proxy_expr_vals)
+export(i3HMM_predict_CNV_via_HMM_on_indiv_cells)
+export(i3HMM_predict_CNV_via_HMM_on_tumor_subclusters)
+export(i3HMM_predict_CNV_via_HMM_on_whole_tumor_samples)
+export(inferCNVBayesNet)
 export(invert_log2)
 export(invert_log2xplus1)
 export(log2xplus1)
 export(make_zero_NA)
 export(mask_non_DE_genes_basic)
 export(mean_center_gene_expr)
-export(ngchm)
 export(normalize_counts_by_seq_depth)
 export(plot_cnv)
+export(predict_CNV_via_HMM_on_indiv_cells)
+export(predict_CNV_via_HMM_on_tumor_subclusters)
+export(predict_CNV_via_HMM_on_whole_tumor_samples)
 export(remove_genes)
 export(remove_genes_at_ends_of_chromosomes)
 export(remove_outliers_norm)
-export(remove_spike)
 export(require_above_min_cells_ref)
 export(require_above_min_mean_expr_cutoff)
+export(returningInferCNV)
 export(run)
-export(scale_cnv_by_spike)
+export(scale_infercnv_expr)
 export(smooth_by_chromosome)
-export(spike_in_variation_chrs)
+export(smooth_by_chromosome_runmeans)
 export(split_references)
 export(subtract_ref_expr_from_obs)
 export(transform_to_reference_based_Zscores)
+exportClasses(MCMC_inferCNV)
 exportClasses(infercnv)
+exportMethods(MeanSD)
+exportMethods(cellGene)
+exportMethods(getGenesCells)
+exportMethods(getProbabilities)
+exportMethods(getStates)
+exportMethods(initializeObject)
+exportMethods(mcmcDiagnosticPlots)
+exportMethods(nonParallel)
+exportMethods(plotProbabilities)
+exportMethods(postProbNormal)
+exportMethods(removeCNV)
+exportMethods(removeCells)
+exportMethods(returningInferCNV)
+exportMethods(runMCMC)
+exportMethods(setBayesMaxPNormal)
+exportMethods(withParallel)
 import(RColorBrewer)
-import(coin)
+import(argparse)
+import(coda)
+import(doParallel)
+import(fitdistrplus)
+import(foreach)
 import(futile.logger)
+import(future)
+import(ggplot2)
+importFrom(BiocGenerics,counts)
+importFrom(BiocGenerics,t)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,colSums)
 importFrom(Matrix,rowMeans)
+importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SummarizedExperiment,"assays<-")
+importFrom(SummarizedExperiment,"colData<-")
+importFrom(SummarizedExperiment,"rowData<-")
+importFrom(SummarizedExperiment,assays)
+importFrom(SummarizedExperiment,colData)
+importFrom(SummarizedExperiment,rowData)
+importFrom(SummarizedExperiment,start)
 importFrom(ape,as.phylo)
 importFrom(ape,write.tree)
-importFrom(binhf,ansc)
+importFrom(caTools,runmean)
+importFrom(coin,oneway_test)
+importFrom(coin,pvalue)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,count)
+importFrom(edgeR,estimateDisp)
 importFrom(fastcluster,hclust)
 importFrom(gplots,bluered)
 importFrom(grDevices,col2rgb)
@@ -67,31 +118,57 @@ importFrom(graphics,points)
 importFrom(graphics,rect)
 importFrom(graphics,text)
 importFrom(graphics,title)
+importFrom(gridExtra,gtable_combine)
+importFrom(gridExtra,marrangeGrob)
+importFrom(gridExtra,tableGrob)
+importFrom(gridExtra,ttheme_default)
 importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,setClass)
+importFrom(parallel,detectCores)
+importFrom(reshape,melt)
+importFrom(rjags,coda.samples)
+importFrom(rjags,jags.model)
 importFrom(stats,as.dendrogram)
 importFrom(stats,as.dist)
 importFrom(stats,complete.cases)
 importFrom(stats,cor)
 importFrom(stats,cutree)
 importFrom(stats,density)
 importFrom(stats,dist)
+importFrom(stats,dnorm)
+importFrom(stats,ecdf)
 importFrom(stats,filter)
+importFrom(stats,ks.test)
+importFrom(stats,lm)
 importFrom(stats,median)
+importFrom(stats,nls)
 importFrom(stats,order.dendrogram)
 importFrom(stats,p.adjust)
+importFrom(stats,pnorm)
 importFrom(stats,predict)
+importFrom(stats,qgamma)
+importFrom(stats,qnorm)
 importFrom(stats,quantile)
+importFrom(stats,rbinom)
+importFrom(stats,rchisq)
 importFrom(stats,reorder)
+importFrom(stats,rgamma)
+importFrom(stats,rlnorm)
+importFrom(stats,rnbinom)
 importFrom(stats,rnorm)
+importFrom(stats,rpois)
 importFrom(stats,runif)
 importFrom(stats,sd)
+importFrom(stats,shapiro.test)
 importFrom(stats,smooth.spline)
 importFrom(stats,t.test)
+importFrom(stats,update)
 importFrom(stats,var)
 importFrom(stats,wilcox.test)
+importFrom(tidyr,gather)
 importFrom(utils,flush.console)
+importFrom(utils,read.csv)
 importFrom(utils,read.table)
 importFrom(utils,tail)
 importFrom(utils,write.table)