adding dataVariance package and updating RLibararies to rel. 88.

arcolombo · arcolombo · commit 6e04a52d419d · 2017-04-11T14:29:48.000-07:00
diff --git a/RLibraries/EnsDbLite.Hsapiens.88/DESCRIPTION b/RLibraries/EnsDbLite.Hsapiens.88/DESCRIPTION
@@ -1,16 +1,16 @@
-Package: EnsDbLite.Hsapiens.84
+Package: EnsDbLite.Hsapiens.88
 Title: Ensembl-based annotation package
 Description: Lightweight Ensembl transcript annotations
 Version: 1.0
-Author: .
-Maintainer: .<dev@null.com>
+Author: Nobody
+Maintainer: Nobody<dev@null.com>
 Depends: TxDbLite
 Imports: GenomicFeatures, RSQLite
 License: Artistic-2.0
 organism: Homo sapiens
 species: Homo sapiens
 provider: Ensembl
 provider_version: GRCh38
-release_date: Tue Apr 12 13:53:44 2016
+release_date: Mon Apr 10 16:28:31 2017
 resource_url: ftp://ftp.ensembl.org/pub/release-GRCh38
 biocViews: AnnotationData, EnsDbLite, Homo_sapiens
diff --git a/RLibraries/EnsDbLite.Hsapiens.88/NAMESPACE b/RLibraries/EnsDbLite.Hsapiens.88/NAMESPACE
@@ -2,7 +2,7 @@
 import(GenomicFeatures)
 import(ensembldb)
 
-### Don't export EnsDbLite.Hsapiens.84 (the object defined in this
+### Don't export EnsDbLite.Hsapiens.88 (the object defined in this
 ### package): it is created and dynamically exported at load time (refer
 ### to R/zzz.R for the details).
 
diff --git a/RLibraries/EnsDbLite.Hsapiens.88/R/zzz.R b/RLibraries/EnsDbLite.Hsapiens.88/R/zzz.R
diff --git a/RLibraries/EnsDbLite.Hsapiens.88/inst/extdata/EnsDbLite.Hsapiens.88.sqlite b/RLibraries/EnsDbLite.Hsapiens.88/inst/extdata/EnsDbLite.Hsapiens.88.sqlite
diff --git a/RLibraries/EnsDbLite.Hsapiens.88/man/package.Rd b/RLibraries/EnsDbLite.Hsapiens.88/man/package.Rd
@@ -1,9 +1,9 @@
-\name{EnsDbLite.Hsapiens.84}
+\name{EnsDbLite.Hsapiens.88}
 \docType{package}
 
-\alias{EnsDbLite.Hsapiens.84-package}
-\alias{EnsDbLite.Hsapiens.84}
-\alias{EnsDbLite.Hsapiens.84}
+\alias{EnsDbLite.Hsapiens.88-package}
+\alias{EnsDbLite.Hsapiens.88}
+\alias{EnsDbLite.Hsapiens.88}
 
 
 \title{Ensembl-based annotation package}
@@ -16,20 +16,20 @@
 
 \note{
   This data package was made from resources at Ensembl on
-  Tue Apr 12 13:53:44 2016 and based on the GRCh38
+  Mon Apr 10 16:28:31 2017 and based on the GRCh38
 }
 
-\author{.}
+\author{Nobody}
 
 
 
 \examples{
 ## load the library
-##library(EnsDbLite.Hsapiens.84)
+##library(EnsDbLite.Hsapiens.88)
 ## list the contents that are loaded into memory
-ls('package:EnsDbLite.Hsapiens.84')
+ls('package:EnsDbLite.Hsapiens.88')
 ## show the db object that is loaded by calling it's name
-EnsDbLite.Hsapiens.84
+EnsDbLite.Hsapiens.88
 
 ## for more examples see the ensembldb package.
 
diff --git a/RLibraries/EnsDbLite.Mmusculus.88/DESCRIPTION b/RLibraries/EnsDbLite.Mmusculus.88/DESCRIPTION
@@ -1,16 +1,16 @@
-Package: EnsDbLite.Mmusculus.84
+Package: EnsDbLite.Mmusculus.88
 Title: Ensembl-based annotation package
 Description: Lightweight Ensembl transcript annotations
 Version: 1.0
-Author: .
-Maintainer: .<dev@null.com>
+Author: Nobody
+Maintainer: Nobody<dev@null.com>
 Depends: TxDbLite
 Imports: GenomicFeatures, RSQLite
 License: Artistic-2.0
 organism: Mus musculus
 species: Mus musculus
 provider: Ensembl
 provider_version: GRCm38
-release_date: Wed Apr 20 15:33:50 2016
+release_date: Mon Apr 10 16:46:04 2017
 resource_url: ftp://ftp.ensembl.org/pub/release-GRCm38
 biocViews: AnnotationData, EnsDbLite, Mus_musculus
diff --git a/RLibraries/EnsDbLite.Mmusculus.88/NAMESPACE b/RLibraries/EnsDbLite.Mmusculus.88/NAMESPACE
@@ -2,7 +2,7 @@
 import(GenomicFeatures)
 import(ensembldb)
 
-### Don't export EnsDbLite.Mmusculus.84 (the object defined in this
+### Don't export EnsDbLite.Mmusculus.88 (the object defined in this
 ### package): it is created and dynamically exported at load time (refer
 ### to R/zzz.R for the details).
 
diff --git a/RLibraries/EnsDbLite.Mmusculus.88/R/zzz.R b/RLibraries/EnsDbLite.Mmusculus.88/R/zzz.R
diff --git a/RLibraries/EnsDbLite.Mmusculus.88/inst/extdata/EnsDbLite.Mmusculus.88.sqlite b/RLibraries/EnsDbLite.Mmusculus.88/inst/extdata/EnsDbLite.Mmusculus.88.sqlite
diff --git a/RLibraries/EnsDbLite.Mmusculus.88/man/package.Rd b/RLibraries/EnsDbLite.Mmusculus.88/man/package.Rd
@@ -1,9 +1,9 @@
-\name{EnsDbLite.Mmusculus.84}
+\name{EnsDbLite.Mmusculus.88}
 \docType{package}
 
-\alias{EnsDbLite.Mmusculus.84-package}
-\alias{EnsDbLite.Mmusculus.84}
-\alias{EnsDbLite.Mmusculus.84}
+\alias{EnsDbLite.Mmusculus.88-package}
+\alias{EnsDbLite.Mmusculus.88}
+\alias{EnsDbLite.Mmusculus.88}
 
 
 \title{Ensembl-based annotation package}
@@ -16,20 +16,20 @@
 
 \note{
   This data package was made from resources at Ensembl on
-  Wed Apr 20 15:33:50 2016 and based on the GRCm38
+  Mon Apr 10 16:46:04 2017 and based on the GRCm38
 }
 
-\author{.}
+\author{Nobody}
 
 
 
 \examples{
 ## load the library
-##library(EnsDbLite.Mmusculus.84)
+##library(EnsDbLite.Mmusculus.88)
 ## list the contents that are loaded into memory
-ls('package:EnsDbLite.Mmusculus.84')
+ls('package:EnsDbLite.Mmusculus.88')
 ## show the db object that is loaded by calling it's name
-EnsDbLite.Mmusculus.84
+EnsDbLite.Mmusculus.88
 
 ## for more examples see the ensembldb package.
 
diff --git a/RLibraries/RepDbLite.Hsapiens.2103/DESCRIPTION b/RLibraries/RepDbLite.Hsapiens.2103/DESCRIPTION
@@ -0,0 +1,16 @@
+Package: RepDbLite.Hsapiens.2103
+Title: RepBase-based annotation package
+Description: lightweight RepBase transcript annotations
+Version: 1.0
+Author: .
+Maintainer: . <dev@null.com>
+Depends: TxDbLite
+Imports: GenomicFeatures, RSQLite
+License: Artistic-2.0
+organism: Homo sapiens
+species: Homo sapiens
+provider: RepBase
+provider_version: RepBase21_03
+release_date: Tue Apr 12 14:17:21 2016
+resource_url: http://www.girinst.org/server/RepBase/protected/RepBaseRepBase21_03.fasta/
+biocViews: AnnotationData, EnsDbLite, Homo_sapiens
diff --git a/RLibraries/RepDbLite.Hsapiens.2103/NAMESPACE b/RLibraries/RepDbLite.Hsapiens.2103/NAMESPACE
@@ -0,0 +1,9 @@
+##import(AnnotationDbi)
+import(GenomicFeatures)
+import(ensembldb)
+
+### Don't export RepDbLite.Hsapiens.2103 (the object defined in this
+### package): it is created and dynamically exported at load time (refer
+### to R/zzz.R for the details).
+
+
diff --git a/RLibraries/RepDbLite.Hsapiens.2103/R/zzz.R b/RLibraries/RepDbLite.Hsapiens.2103/R/zzz.R
@@ -0,0 +1,18 @@
+###
+### Load any db objects whenever the package is loaded.
+###
+.onLoad <- function(libname, pkgname)
+{
+  ns <- asNamespace(pkgname)
+  path <- system.file("extdata", package=pkgname, lib.loc=libname)
+  files <- dir(path)
+  for(i in seq_len(length(files))){
+   # db <- RepDbLite(system.file("extdata", files[[i]], package=pkgname,
+    #                            lib.loc=libname))
+    db<-RepDbLite(files[[i]],path)
+    objname <- sub(".sqlite$","",files[[i]])
+    assign(objname, db, envir=ns)
+    namespaceExport(ns, objname)
+  }
+}
+
diff --git a/RLibraries/RepDbLite.Hsapiens.2103/inst/extdata/RepDbLite.Hsapiens.2103.sqlite b/RLibraries/RepDbLite.Hsapiens.2103/inst/extdata/RepDbLite.Hsapiens.2103.sqlite
diff --git a/RLibraries/RepDbLite.Hsapiens.2103/man/package.Rd b/RLibraries/RepDbLite.Hsapiens.2103/man/package.Rd
@@ -0,0 +1,40 @@
+\name{RepDbLite.Hsapiens.2103}
+\docType{package}
+
+\alias{RepDbLite.Hsapiens.2103-package}
+\alias{RepDbLite.Hsapiens.2103}
+\alias{RepDbLite.Hsapiens.2103}
+
+
+\title{RepBase-based annotation package}
+
+\description{
+  This package loads an SQL connection to a database containing
+  annotations from Ensembl. For examples and help on functions see the
+  help pages from the \code{ensembldb} package!
+}
+
+\note{
+  This data package was made from resources at RepBase on
+  Tue Apr 12 14:17:21 2016 and based on the RepBase21_03
+}
+
+\author{.}
+
+
+
+\examples{
+## load the library
+##library(RepDbLite.Hsapiens.2103)
+## list the contents that are loaded into memory
+ls('package:RepDbLite.Hsapiens.2103')
+## show the db object that is loaded by calling it's name
+RepDbLite.Hsapiens.2103
+
+## for more examples see the ensembldb package.
+
+
+}
+
+\keyword{package}
+\keyword{data}
diff --git a/RLibraries/RepDbLite.Mmusculus.2103/DESCRIPTION b/RLibraries/RepDbLite.Mmusculus.2103/DESCRIPTION
@@ -0,0 +1,16 @@
+Package: RepDbLite.Mmusculus.2103
+Title: RepBase-based annotation package
+Description: lightweight RepBase transcript annotations
+Version: 1.0
+Author: .
+Maintainer: . <dev@null.com>
+Depends: TxDbLite
+Imports: GenomicFeatures, RSQLite
+License: Artistic-2.0
+organism: Mus musculus
+species: Mus musculus
+provider: RepBase
+provider_version: RepBase21_03
+release_date: Wed Apr 20 11:13:10 2016
+resource_url: http://www.girinst.org/server/RepBase/protected/RepBaseRepBase21_03.fasta/
+biocViews: AnnotationData, EnsDbLite, Mus_musculus
diff --git a/RLibraries/RepDbLite.Mmusculus.2103/NAMESPACE b/RLibraries/RepDbLite.Mmusculus.2103/NAMESPACE
@@ -0,0 +1,9 @@
+##import(AnnotationDbi)
+import(GenomicFeatures)
+import(ensembldb)
+
+### Don't export RepDbLite.Mmusculus.2103 (the object defined in this
+### package): it is created and dynamically exported at load time (refer
+### to R/zzz.R for the details).
+
+
diff --git a/RLibraries/RepDbLite.Mmusculus.2103/R/zzz.R b/RLibraries/RepDbLite.Mmusculus.2103/R/zzz.R
@@ -0,0 +1,18 @@
+###
+### Load any db objects whenever the package is loaded.
+###
+.onLoad <- function(libname, pkgname)
+{
+  ns <- asNamespace(pkgname)
+  path <- system.file("extdata", package=pkgname, lib.loc=libname)
+  files <- dir(path)
+  for(i in seq_len(length(files))){
+   # db <- RepDbLite(system.file("extdata", files[[i]], package=pkgname,
+    #                            lib.loc=libname))
+    db<-RepDbLite(files[[i]],path)
+    objname <- sub(".sqlite$","",files[[i]])
+    assign(objname, db, envir=ns)
+    namespaceExport(ns, objname)
+  }
+}
+
diff --git a/RLibraries/RepDbLite.Mmusculus.2103/inst/extdata/RepDbLite.Mmusculus.2103.sqlite b/RLibraries/RepDbLite.Mmusculus.2103/inst/extdata/RepDbLite.Mmusculus.2103.sqlite
diff --git a/RLibraries/RepDbLite.Mmusculus.2103/man/package.Rd b/RLibraries/RepDbLite.Mmusculus.2103/man/package.Rd
@@ -0,0 +1,40 @@
+\name{RepDbLite.Mmusculus.2103}
+\docType{package}
+
+\alias{RepDbLite.Mmusculus.2103-package}
+\alias{RepDbLite.Mmusculus.2103}
+\alias{RepDbLite.Mmusculus.2103}
+
+
+\title{RepBase-based annotation package}
+
+\description{
+  This package loads an SQL connection to a database containing
+  annotations from Ensembl. For examples and help on functions see the
+  help pages from the \code{ensembldb} package!
+}
+
+\note{
+  This data package was made from resources at RepBase on
+  Wed Apr 20 11:13:10 2016 and based on the RepBase21_03
+}
+
+\author{.}
+
+
+
+\examples{
+## load the library
+##library(RepDbLite.Mmusculus.2103)
+## list the contents that are loaded into memory
+ls('package:RepDbLite.Mmusculus.2103')
+## show the db object that is loaded by calling it's name
+RepDbLite.Mmusculus.2103
+
+## for more examples see the ensembldb package.
+
+
+}
+
+\keyword{package}
+\keyword{data}
diff --git a/arkasAnalysisBaseSpace/R/findChildTranscriptInput.R b/arkasAnalysisBaseSpace/R/findChildTranscriptInput.R
@@ -16,11 +16,11 @@ transcript<-unlist(strsplit(unlist(transcriptInput),",")) #vector with length eq
 hash=new.env(hash=TRUE,parent=emptyenv(),size=100L)
 transcriptomeValue<-list()
 transcriptomeValue[[1]]<-"ERCC.fa.gz"
-transcriptomeValue[2]<-"Homo_sapiens.GRCh38.84.cdna.all.fa.gz"
-transcriptomeValue[[2]][2]<-"Homo_sapiens.GRCh38.84.ncrna.fa.gz"
+transcriptomeValue[2]<-"Homo_sapiens.GRCh38.88.cdna.all.fa.gz"
+transcriptomeValue[[2]][2]<-"Homo_sapiens.GRCh38.88.ncrna.fa.gz"
 transcriptomeValue[3]<-"Homo_sapiens.RepBase.21_03.merged.fa.gz"
-transcriptomeValue[4]<-"Mus_musculus.GRCm38.84.cdna.all.fa.gz"
-transcriptomeValue[[4]][2]<-"Mus_musculus.GRCm38.84.ncrna.fa.gz"
+transcriptomeValue[4]<-"Mus_musculus.GRCm38.88.cdna.all.fa.gz"
+transcriptomeValue[[4]][2]<-"Mus_musculus.GRCm38.88.ncrna.fa.gz"
 transcriptomeValue[5]<-"Mus_musculus.RepBase.21_03.merged.fa.gz"
 #transcriptomeValue[[5]][2]<-"Mus_musculus.RepBase.v20_05.rodrep.fa.gz"
 transcriptomeValue[6]<-"Drosophila_melanogaster.BDGP6.81.cdna.all.fa.gz"
diff --git a/arkasAnalysisBaseSpace/R/findTranscriptInput.R b/arkasAnalysisBaseSpace/R/findTranscriptInput.R
@@ -9,11 +9,11 @@ transcriptInput<-fileJSON$Properties$Items$Items[which(selectNames=="Input.check
 hash=new.env(hash=TRUE,parent=emptyenv(),size=100L)
 transcriptomeValue<-list()
 transcriptomeValue[[1]]<-"ERCC.fa.gz"
-transcriptomeValue[2]<-"Homo_sapiens.GRCh38.84.cdna.all.fa.gz"
-transcriptomeValue[[2]][2]<-"Homo_sapiens.GRCh38.84.ncrna.fa.gz"
+transcriptomeValue[2]<-"Homo_sapiens.GRCh38.88.cdna.all.fa.gz"
+transcriptomeValue[[2]][2]<-"Homo_sapiens.GRCh38.88.ncrna.fa.gz"
 transcriptomeValue[3]<-"Homo_sapiens.RepBase.21_03.merged.fa.gz"
-transcriptomeValue[4]<-"Mus_musculus.GRCm38.84.cdna.all.fa.gz"
-transcriptomeValue[[4]][2]<-"Mus_musculus.GRCm38.84.ncrna.fa.gz"
+transcriptomeValue[4]<-"Mus_musculus.GRCm38.88.cdna.all.fa.gz"
+transcriptomeValue[[4]][2]<-"Mus_musculus.GRCm38.88.ncrna.fa.gz"
 transcriptomeValue[5]<-"Mus_musculus.RepBase.21_03.merged.fa.gz"
 #transcriptomeValue[[5]][2]<-"Mus_musculus.RepBase.v20_05.rodrep.fa.gz"
 transcriptomeValue[6]<-"Drosophila_melanogaster.BDGP6.81.cdna.all.fa.gz"
diff --git a/arkasBasespace/R/createChildAppSession.R b/arkasBasespace/R/createChildAppSession.R
@@ -67,10 +67,10 @@ stopifnot(all(appSession$samples %in% dir(scratchPath)[!grepl(".json",dir(scratc
 if(all(is.na(unlist(fileJSON$Properties$Items$Items[which(selectNames=="Input.app-result-id")])))==TRUE) {
 print("Detected No user Fasta input...")
   if(jsonSpecies=="Mus.musculus"){
-   appSession$indexName<-"ERCC_mergedWith_Mus_musculus.GRCm38.84.cdna.all_mergedWith_Mus_musculus.GRCm38.84.ncrna_mergedWith_Mus_musculus.RepBase.21_03.mergedkallisto.0.42.4.fa.kidx"  
+   appSession$indexName<-"ERCC_mergedWith_Mus_musculus.GRCm38.88.cdna.all_mergedWith_Mus_musculus.GRCm38.88.ncrna_mergedWith_Mus_musculus.RepBase.21_03.mergedkallisto.0.43.0.fa.kidx"  
    }
   if(jsonSpecies=="Homo.sapiens"){
-   appSession$indexName<-"ERCC_mergedWith_Homo_sapiens.GRCh38.84.cdna.all_mergedWith_Homo_sapiens.GRCh38.84.ncrna_mergedWith_Homo_sapiens.RepBase.21_03.mergedkallisto.0.42.4.fa.kidx"
+   appSession$indexName<-"ERCC_mergedWith_Homo_sapiens.GRCh38.88.cdna.all_mergedWith_Homo_sapiens.GRCh38.88.ncrna_mergedWith_Homo_sapiens.RepBase.21_03.mergedkallisto.0.43.0.fa.kidx"
     }
 }
 #if(!any(is.na(unlist(fileJSON$Properties$Items$Items[which(selectNames=="Input.app-result-id")])))==TRUE) {
diff --git a/arkasBasespace/R/findTranscriptInput.R b/arkasBasespace/R/findTranscriptInput.R
@@ -9,11 +9,11 @@ transcriptInput<-fileJSON$Properties$Items$Items[which(selectNames=="Input.check
 hash=new.env(hash=TRUE,parent=emptyenv(),size=100L)
 transcriptomeValue<-list()
 transcriptomeValue[[1]]<-"ERCC.fa.gz"
-transcriptomeValue[2]<-"Homo_sapiens.GRCh38.84.cdna.all.fa.gz"
-transcriptomeValue[[2]][2]<-"Homo_sapiens.GRCh38.84.ncrna.fa.gz"
+transcriptomeValue[2]<-"Homo_sapiens.GRCh38.88.cdna.all.fa.gz"
+transcriptomeValue[[2]][2]<-"Homo_sapiens.GRCh38.88.ncrna.fa.gz"
 transcriptomeValue[3]<-"Homo_sapiens.RepBase.21_03.merged.fa.gz"
-transcriptomeValue[4]<-"Mus_musculus.GRCm38.84.cdna.all.fa.gz"
-transcriptomeValue[[4]][2]<-"Mus_musculus.GRCm38.84.ncrna.fa.gz"
+transcriptomeValue[4]<-"Mus_musculus.GRCm38.88.cdna.all.fa.gz"
+transcriptomeValue[[4]][2]<-"Mus_musculus.GRCm38.88.ncrna.fa.gz"
 transcriptomeValue[5]<-"Mus_musculus.RepBase.21_03.merged.fa.gz"
 #transcriptomeValue[[5]][2]<-"Mus_musculus.RepBase.v20_05.rodrep.fa.gz"
 transcriptomeValue[6]<-"Drosophila_melanogaster.BDGP6.81.cdna.all.fa.gz"
diff --git a/dataVariance b/dataVariance
@@ -0,0 +1 @@
+Subproject commit c47f024deeb895874632ad6254d430b0a4e86c84
diff --git a/outputReport/generateOutputResults.Rmd b/outputReport/generateOutputResults.Rmd
@@ -1,6 +1,6 @@
 ---
 title: "Arkas: Transcript Abundance Quantification In Much Less Time"
-author:  "Anthony R. Colombo, Timothy J. Triche, Jr, Harold Pimentel"
+author:  "Anthony R. Colombo, Timothy J. Triche, Jr, Giridharan Ramsingh"
 output:
     html_document:
       toc: true
@@ -9,9 +9,9 @@ date: "`r format(Sys.time(), '%d %B, %Y')`"
 ---
 
 # Output Report
-Arkas-Quantification is the first step in obtaining analytical results from raw reads.  For Analytical results, please use the second application called Arkas-Analysis which can generate gene expression heatmaps, Reactome gene set enrichment analysis, and RUV normalization.  This application supports single cell experiments.   This output report merely displays the kallisto version used in quantifying transcripts used in parallel.  Please cite : http://biorxiv.org/content/early/2016/04/06/031435
+Arkas-Quantification is the first step in obtaining analytical results from raw reads.  For Analytical results, please use the second application called Arkas-Analysis which can generate gene expression heatmaps, Reactome gene set enrichment analysis, and RUV normalization.  This application supports single cell experiments.   This output report merely displays the kallisto version used in quantifying transcripts used in parallel.  
 
-#Kallisto Version
+# Kallisto Version
 The kallisto version used for Arkas Quantification is:
 ```
 kallisto, version 0.43.0
