Merge branch 'dev'

DESCRIPTION

@@ -1,17 +1,20 @@
 Package: psichomics
 Title: Graphical Interface for Alternative Splicing Quantification, Analysis and
     Visualisation
-Version: 1.8.1
+Version: 1.8.2
 Encoding: UTF-8
-Authors@R: c( person("Nuno", "Saraiva-Agostinho", ,
-        "nunodanielagostinho@gmail.com", role = c("aut", "cre")),
-        person(c("Nuno", "Luís"), "Barbosa-Morais",
-        role=c("aut", "led", "ths")),
-        person("André", "Falcão", role="ths"), person("Lina",
-        "Gallego Paez", role="ctb"), person("Marie", "Bordone",
-        role="ctb"), person("Teresa", "Maia", role="ctb"),
-        person("Mariana", "Ferreira", role="ctb"), person("Ana Carolina", 
-        "Leote", role="ctb"), person("Bernardo", "de Almeida", role="ctb"))
+Authors@R: c(
+        person("Nuno", "Saraiva-Agostinho",
+            email="nunodanielagostinho@gmail.com", role = c("aut", "cre")),
+        person(c("Nuno", "Luís"), "Barbosa-Morais", 
+            role=c("aut", "led", "ths")),
+        person("André", "Falcão", role="ths"), 
+        person("Lina", "Gallego Paez", role="ctb"), 
+        person("Marie", "Bordone", role="ctb"), 
+        person("Teresa", "Maia", role="ctb"),
+        person("Mariana", "Ferreira", role="ctb"),
+        person("Ana Carolina", "Leote", role="ctb"), 
+        person("Bernardo", "de Almeida", role="ctb"))
 Description: Interactive R package with an intuitive Shiny-based graphical 
     interface for alternative splicing quantification and integrative analyses 
     of alternative splicing and gene expression based on The Cancer Genome Atlas
@@ -28,8 +31,9 @@ Depends:
     shinyBS
 License: MIT + file LICENSE
 LazyData: true
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 Imports:
+    AnnotationDbi,
     AnnotationHub,
     cluster,
     colourpicker,
@@ -42,6 +46,7 @@ Imports:
     fastmatch,
     ggplot2,
     ggrepel,
+    graphics,
     grDevices,
     highcharter (>= 0.5.0),
     htmltools,
@@ -54,6 +59,7 @@ Imports:
     Rcpp (>= 0.12.14),
     recount,
     R.utils,
+    reshape2,
     shinyjs,
     stringr,
     stats,
@@ -63,7 +69,8 @@ Imports:
     utils,
     XML,
     xtable,
-    methods
+    methods,
+    org.Hs.eg.db
 Suggests:
     testthat,
     knitr,

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2015-2018
+YEAR: 2015-2019
 COPYRIGHT HOLDER: Nuno Agostinho

NAMESPACE

@@ -1,20 +1,28 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method("[",GEandAScorrelation)
+S3method(as.table,GEandAScorrelation)
+S3method(plot,GEandAScorrelation)
+S3method(print,GEandAScorrelation)
 export(assignValuePerPatient)
 export(assignValuePerSubject)
 export(calculateLoadingsContribution)
+export(convertGeneIdentifiers)
 export(correlateGEandAS)
 export(createGroupByAttribute)
 export(createGroupByColumn)
 export(diffAnalyses)
 export(ensemblToUniprot)
+export(filterGeneExpr)
 export(filterGroups)
+export(filterPSI)
 export(getAttributesTime)
 export(getColumnsTime)
 export(getDownloadsFolder)
 export(getFirebrowseCohorts)
 export(getFirebrowseDataTypes)
 export(getFirebrowseDates)
+export(getGeneList)
 export(getGenesFromSplicingEvents)
 export(getGtexTissues)
 export(getMatchingSamples)
@@ -37,6 +45,7 @@ export(loadAnnotation)
 export(loadFirebrowseData)
 export(loadGtexData)
 export(loadLocalFiles)
+export(loadSRAproject)
 export(normaliseGeneExpression)
 export(optimalPSIcutoff)
 export(optimalSurvivalCutoff)
@@ -52,11 +61,14 @@ export(performICA)
 export(performPCA)
 export(plotCorrelation)
 export(plotDistribution)
+export(plotGeneExprPerSample)
 export(plotGroupIndependence)
 export(plotICA)
 export(plotPCA)
 export(plotProtein)
+export(plotRowStats)
 export(plotSurvivalCurves)
+export(plotSurvivalPvaluesByCutoff)
 export(plotTranscripts)
 export(plotVariance)
 export(prepareAnnotationFromEvents)
@@ -75,6 +87,8 @@ export(survdiff.survTerms)
 export(survfit.survTerms)
 export(testGroupIndependence)
 export(testSurvival)
+exportMethods(colSums)
+importFrom(AnnotationDbi,select)
 importFrom(AnnotationHub,AnnotationHub)
 importFrom(AnnotationHub,query)
 importFrom(DT,JS)
@@ -85,6 +99,7 @@ importFrom(DT,replaceData)
 importFrom(DT,selectRows)
 importFrom(R.utils,capitalize)
 importFrom(R.utils,evalWithTimeout)
+importFrom(R.utils,gunzip)
 importFrom(Rcpp,sourceCpp)
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,end)
@@ -102,15 +117,18 @@ importFrom(cluster,pam)
 importFrom(cluster,silhouette)
 importFrom(colourpicker,colourInput)
 importFrom(colourpicker,updateColourInput)
+importFrom(data.table,data.table)
 importFrom(data.table,fread)
 importFrom(data.table,fwrite)
 importFrom(data.table,setkeyv)
 importFrom(data.table,setnames)
 importFrom(data.table,setorderv)
 importFrom(digest,digest)
+importFrom(edgeR,"[.DGEList")
 importFrom(edgeR,DGEList)
 importFrom(edgeR,calcNormFactors)
 importFrom(edgeR,cpm)
+importFrom(edgeR,filterByExpr)
 importFrom(fastICA,fastICA)
 importFrom(fastmatch,"%fin%")
 importFrom(fastmatch,fmatch)
@@ -121,9 +139,11 @@ importFrom(ggplot2,coord_equal)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_density_2d)
+importFrom(ggplot2,geom_hline)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
@@ -132,8 +152,11 @@ importFrom(ggplot2,scale_fill_gradient2)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_light)
 importFrom(ggplot2,unit)
+importFrom(ggplot2,xlim)
+importFrom(ggplot2,ylim)
 importFrom(ggrepel,geom_label_repel)
 importFrom(grDevices,chull)
+importFrom(graphics,plot)
 importFrom(highcharter,"%>%")
 importFrom(highcharter,JS)
 importFrom(highcharter,fa_icon_mark)
@@ -171,16 +194,19 @@ importFrom(jsonlite,toJSON)
 importFrom(limma,eBayes)
 importFrom(limma,lmFit)
 importFrom(limma,topTable)
+importFrom(limma,voom)
 importFrom(methods,is)
 importFrom(miscTools,colMedians)
 importFrom(miscTools,rowMedians)
+importFrom(org.Hs.eg.db,org.Hs.eg.db)
 importFrom(pairsD3,pairsD3)
 importFrom(pairsD3,pairsD3Output)
 importFrom(pairsD3,renderPairsD3)
 importFrom(plyr,dlply)
 importFrom(plyr,ldply)
 importFrom(plyr,rbind.fill)
 importFrom(recount,download_study)
+importFrom(reshape2,melt)
 importFrom(shiny,HTML)
 importFrom(shiny,NS)
 importFrom(shiny,Progress)
@@ -298,6 +324,7 @@ importFrom(stats,kruskal.test)
 importFrom(stats,lm)
 importFrom(stats,loess.smooth)
 importFrom(stats,median)
+importFrom(stats,na.omit)
 importFrom(stats,optim)
 importFrom(stats,p.adjust)
 importFrom(stats,pchisq)
@@ -314,6 +341,7 @@ importFrom(survival,survdiff)
 importFrom(survival,survfit)
 importFrom(tools,file_ext)
 importFrom(tools,file_path_sans_ext)
+importFrom(utils,askYesNo)
 importFrom(utils,download.file)
 importFrom(utils,head)
 importFrom(utils,read.delim)

NEWS

@@ -1,3 +1,93 @@
+# 1.8.2 (26 March, 2019)
+
+* Data loading:
+    - GTEx data can now be automatically downloaded and loaded on-demand
+    - By default, data table now only displays at most the first 100 columns 
+    for performance reasons
+* Alternative splicing quantification:
+    - Allow to discard samples before alternative splicing quantification
+    - In alternative splicing quantification dataset summary, plot
+    quantification based on median, variance and range per splicing event across
+    samples to provide tools to filter quantification (`plotRowStats()`)
+* Gene expression filtering and normalisation:
+    - Allow to discard samples before filtering and normalisation
+    - Filter low read counts using `edgeR::filterByExpr()`
+    - Allow to perform `limma::voom()` on gene expression data (without design
+    matrix) and to apply its normalisation methods
+    - In gene expression dataset summary, plot distribution of gene expression 
+    per sample, distribution of library sizes and gene-wise mean and variance of
+    gene expression across samples to provide the user tools to assess gene 
+    expression normalisation (`plotGeneExprPerSample()`, `plotDistribution()` 
+    and  `plotRowStats()`, respectively)
+    - Convert between different gene identifiers (the original identifier is 
+    kept in some conditions, read `convertGeneIdentifiers()`); in the visual
+    interface, when filtering and normalising gene expression, ENSEMBL 
+    identifiers are converted to gene symbols, by default
+* Groups:
+    - By default, load pre-made lists of genes when loading gene expression or
+    loading/performing alternative splicing quantification
+    - Added pre-made list of genes that encode for RNA-binding proteins 
+    (Sebestyen et al. 2016), useful to postulate about the regulatory role of
+    those proteins based on gene expression and PSI correlation analyses
+* Correlation analyses:
+    - Allow to use groups of genes and alternative splicing events in 
+    correlation analyses
+    - Plot specific combinations of gene and alternative splicing events 
+    (`[.GEandAScorrelation`())
+    - Display progress when performing correlation analyses
+    - Display correlation results in a table (`as.table()`)
+* Survival:
+    - Render p-value plot by cutoff in command-line interface 
+    (`plotSurvivalPvaluesByCutoff()`)
+* Gene, transcript and protein information:
+    - Modify keywords used to search for PubMed articles
+
+## Bug fixes and minor changes
+
+* Improve console logging of error and warning alerts
+* Fix crash when loading psichomics with test data that is not locally available
+(by automatically downloading said data if not found)
+* Allow to edit file path in file/directory browser elemnts
+* Documentation:
+    - Export functions mentioned in the documentation
+    - Hide documentation of internal functions from the PDF reference manual
+* Loading SRA data:
+    - Accept a vector of files as the first argument (easier to use with 
+    `list.files()`)
+    - Ask to overwrite file if one exists with the same name as the output file
+* Groups:
+    - Automatically set dropdown width for group attribute selection
+    - Minor improvements to the group creation interface
+    - Fix error when creating groups containing only samples and no matching 
+    subjects
+    - Fix warning when displaying group preview only based on subjects or 
+    samples
+* Alternative splicing quantification:
+    - Automatically set the human genome version after loading data from TCGA
+    (hg19), GTEx (hg19) or recount2 (hg38)
+    - Fix progress bar
+    - Decrease loading time after quantifying alternative splicing
+    - By default, quantify skipped exons, mutually exclusive exons, alternative 
+    3' and 5' splice sites, and alternative first and last exons; the default
+    option is now consistent across both the visual and command-line interfaces)
+* Differential analyses:
+    - Allow distribution plots to show the name of the samples when hovering or
+    when a rug plot is rendered if `rugLabels = TRUE` (function
+    `plotDistribution()`)
+    - Fix distribution plots requiring all samples in a group when using 
+    function `plotDistribution()`
+    - Fix group colours and opacity for rug plot points within the distribution 
+    plot (occured in the command-line version; function `plotDistribution()`)
+    - Fix wrong information in the table of differential splicing results (only
+    occurs when the first splicing event is one for which there is not enough
+    information to calculate statistical tests)
+    - Fix inconsistency when presenting median and variance differences between
+    gene expression and alternative splicing quantification
+    - Fix error when groups contain samples outside the data being analysed
+* Gene, transcript and protein information:
+    - Fix article title formatting (e.g. bold and italics)
+* Update psichomics citation with journal publication date
+
 # 1.8.1 (3 December, 2018)
 
 * Add tag ImmunoOncology to BiocViews
@@ -171,8 +261,8 @@ hg19 and hg38 annotation that is now available for use with psichomics)
     - Fix splicing events not being quantified based on GTEx v7 junction reads
 * Gene expression normalisation:
     - Fix misleading gene expression (non-)normalisation by converting reads to 
-    counts per million (CPM) using `edgeR::cpm` after normalisation using
-    `edgeR::calcNormFactor`
+    counts per million (CPM) using `edgeR::cpm()` after normalisation using
+    `edgeR::calcNormFactor()`
 * Alternative splicing quantification:
     - Updated support to properly parse new notation of alternative splicing 
     annotation from Bioconductor (backwards compatible with older notation)
@@ -204,7 +294,7 @@ hg19 and hg38 annotation that is now available for use with psichomics)
     tissues are loaded by default)
     - Quantify splicing based on a list of genes (splicing events within all 
     genes are quantified by default)
-    - Parse sample information from TCGA samples using `parseTcgaSampleInfo`
+    - Parse sample information from TCGA samples using `parseTcgaSampleInfo()`
     - Generate TCGA sample metadata when loading TCGA junction quantification
     - Present data summary after loading the data
 * Data grouping: