Several fixes, improvements in documentation

rcastelo · Apr 22, 2024 · b720afb · b720afb
1 parent e8a553a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,18 @@
 Package: atena
 Type: Package
 Title: Analysis of Transposable Elements
-Version: 1.9.5
+Version: 1.9.6
 Authors@R: c(
-  person("Beatriz", "Calvo-Serra", email = "[email protected]", role = c("aut","cre")),
-  person("Robert", "Castelo", email = "[email protected]", role = c("aut")))
-Description: Quantify expression of transposable elements (TEs) from RNA-seq data through
-    different methods, including ERVmap, TEtranscripts and Telescope. A common interface
-    is provided to use each of these methods, which consists of building a parameter object,
-    calling the quantification function with this object and getting a SummarizedExperiment
-    object as output container of the quantified expression profiles. The implementation
+    person("Beatriz", "Calvo-Serra", email="[email protected]",
+           role=c("aut", "cre")),
+    person("Robert", "Castelo", email="[email protected]",
+           role=c("aut")))
+Description: Quantify expression of transposable elements (TEs) from RNA-seq
+    data through different methods, including ERVmap, TEtranscripts and
+    Telescope. A common interface is provided to use each of these methods,
+    which consists of building a parameter object, calling the quantification
+    function with this object and getting a SummarizedExperiment object as
+    output container of the quantified expression profiles. The implementation
     allows one to quantify TEs and gene transcripts in an integrated manner.
 License: Artistic-2.0
 Encoding: UTF-8

diff --git a/NAMESPACE b/NAMESPACE
@@ -34,9 +34,11 @@ importFrom(BiocGenerics,basename)
 importFrom(BiocGenerics,path)
 importFrom(BiocParallel,SerialParam)
 importFrom(BiocParallel,bplapply)
+importFrom(GenomeInfoDb,"genome<-")
 importFrom(GenomeInfoDb,"seqinfo<-")
 importFrom(GenomeInfoDb,"seqlevels<-")
 importFrom(GenomeInfoDb,"seqlevelsStyle<-")
+importFrom(GenomeInfoDb,genome)
 importFrom(GenomeInfoDb,keepSeqlevels)
 importFrom(GenomeInfoDb,seqinfo)
 importFrom(GenomeInfoDb,seqlengths)
@@ -96,6 +98,7 @@ importFrom(S4Vectors,List)
 importFrom(S4Vectors,Rle)
 importFrom(S4Vectors,countQueryHits)
 importFrom(S4Vectors,countSubjectHits)
+importFrom(S4Vectors,decode)
 importFrom(S4Vectors,first)
 importFrom(S4Vectors,from)
 importFrom(S4Vectors,isSorted)

diff --git a/R/AllClasses.R b/R/AllClasses.R
@@ -33,14 +33,14 @@
 #' @examples
 #' bamfiles <- list.files(system.file("extdata", package="atena"),
 #'                        pattern="*.bam", full.names=TRUE)
-#' rmskat <- annotaTEs(genome = "dm6", parsefun = rmskatenaparser, 
-#'                     strict = FALSE, insert = 500)
-#' rmskLTR <- getLTRs(rmskat, relLength = 0.8, 
-#'                    full_length = TRUE, 
-#'                    partial = TRUE)
-#' ttpar <- TEtranscriptsParam(bamfiles, 
-#'                             teFeatures = rmskLTR,
-#'                             singleEnd = TRUE, 
+#' rmskat <- annotaTEs(genome="dm6", parsefun=rmskatenaparser,
+#'                     strict=FALSE, insert=500)
+#' rmskLTR <- getLTRs(rmskat, relLength=0.8,
+#'                    fullLength=TRUE,
+#'                    partial=TRUE)
+#' ttpar <- TEtranscriptsParam(bamfiles,
+#'                             teFeatures=rmskLTR,
+#'                             singleEnd=TRUE,
 #'                             ignoreStrand=TRUE)
 #' path(ttpar)
 #'

diff --git a/R/ERVmap.R b/R/ERVmap.R
@@ -113,16 +113,16 @@
 #' @examples
 #' bamfiles <- list.files(system.file("extdata", package="atena"),
 #'                        pattern="*.bam", full.names=TRUE)
-#' rmskat <- annotaTEs(genome="dm6", parsefun=rmskatenaparser, 
+#' rmskat <- annotaTEs(genome="dm6", parsefun=rmskatenaparser,
 #'                     strict=FALSE, insert=500)
-#' rmskLTR <- getLTRs(rmskat, relLength=0.8, 
-#'                    full_length=TRUE, 
+#' rmskLTR <- getLTRs(rmskat, relLength=0.8,
+#'                    fullLength=TRUE,
 #'                    partial=TRUE,
 #'                    otherLTR=TRUE)
-#' empar <- ERVmapParam(bamfiles, 
-#'                      teFeatures=rmskLTR, 
-#'                      singleEnd=TRUE, 
-#'                      ignoreStrand=TRUE, 
+#' empar <- ERVmapParam(bamfiles,
+#'                      teFeatures=rmskLTR,
+#'                      singleEnd=TRUE,
+#'                      ignoreStrand=TRUE,
 #'                      suboptimalAlignmentCutoff=NA)
 #' empar
 #'
@@ -299,9 +299,9 @@ setMethod("qtex", "ERVmapParam",
                                 verbose, avtags) {
 open(bf)
 while (length(alnreads <- do.call(readfun,
-                                c(list(file = bf), list(param=param),
-                                list(strandMode=empar@strandMode)[strand_arg],
-                                list(use.names=(!avsoas || avgene)))))) {
+                                  c(list(file = bf), list(param=param),
+                                  list(strandMode=empar@strandMode)[strand_arg],
+                                  list(use.names=(!avsoas || avgene)))))) {
     alnreads <- .matchSeqinfo(alnreads, features(empar))
     n <- n + length(alnreads)
     thissalnmask <- .secondaryAlignmentMask(alnreads) #secondary alignment mask

diff --git a/R/TEtranscripts.R b/R/TEtranscripts.R
@@ -87,20 +87,20 @@
 #' @examples
 #' bamfiles <- list.files(system.file("extdata", package="atena"),
 #'                        pattern="*.bam", full.names=TRUE)
-#' rmskat <- annotaTEs(genome="dm6", parsefun=rmskatenaparser, 
+#' rmskat <- annotaTEs(genome="dm6", parsefun=rmskatenaparser,
 #'                     strict=FALSE, insert=500)
-#' rmskLTR <- getLTRs(rmskat, relLength=0.8, 
-#'                    full_length=TRUE, 
+#' rmskLTR <- getLTRs(rmskat, relLength=0.8,
+#'                    fullLength=TRUE,
 #'                    partial=TRUE,
 #'                    otherLTR=TRUE)
 #' library(TxDb.Dmelanogaster.UCSC.dm6.ensGene)
 #' txdb <- TxDb.Dmelanogaster.UCSC.dm6.ensGene
 #' txdb_genes <- genes(txdb)
-#' ttpar <- TEtranscriptsParam(bamfiles, 
+#' ttpar <- TEtranscriptsParam(bamfiles,
 #'                             teFeatures=rmskLTR,
 #'                             geneFeatures=txdb_genes,
-#'                             singleEnd=TRUE, 
-#'                             ignoreStrand=TRUE, 
+#'                             singleEnd=TRUE,
+#'                             ignoreStrand=TRUE,
 #'                             aggregateby="repName")
 #' ttpar
 #'

diff --git a/R/Telescope.R b/R/Telescope.R
@@ -116,15 +116,15 @@
 #' @examples
 #' bamfiles <- list.files(system.file("extdata", package="atena"),
 #'                        pattern="*.bam", full.names=TRUE)
-#' rmskat <- annotaTEs(genome="dm6", parsefun=rmskatenaparser, 
+#' rmskat <- annotaTEs(genome="dm6", parsefun=rmskatenaparser,
 #'                     strict=FALSE, insert=500)
-#' rmskLTR <- getLTRs(rmskat, relLength=0.8, 
-#'                    full_length=TRUE, 
+#' rmskLTR <- getLTRs(rmskat, relLength=0.8,
+#'                    fullLength=TRUE,
 #'                    partial=TRUE,
 #'                    otherLTR=TRUE)
-#' tspar <- TelescopeParam(bfl=bamfiles, 
-#'                         teFeatures=rmskLTR, 
-#'                         singleEnd=TRUE, 
+#' tspar <- TelescopeParam(bfl=bamfiles,
+#'                         teFeatures=rmskLTR,
+#'                         singleEnd=TRUE,
 #'                         ignoreStrand=TRUE)
 #' tspar
 #'