Documentation fixes

DESCRIPTION

@@ -25,9 +25,11 @@ LinkingTo:
     Rcpp
 Imports: 
     Biostrings,
+    GenomeInfoDb,
     methods,
     Rcpp,
-    rtracklayer
+    rtracklayer,
+    S4Vectors
 Depends:
     GenomicRanges,
     R (>= 2.10)

NAMESPACE

@@ -8,9 +8,19 @@ import(methods)
 importFrom(Biostrings,DNAStringSet)
 importFrom(Biostrings,readDNAStringSet)
 importFrom(Biostrings,reverseComplement)
+importFrom(GenomeInfoDb,"genome<-")
+importFrom(GenomeInfoDb,"seqinfo<-")
+importFrom(GenomeInfoDb,"seqlengths<-")
+importFrom(GenomeInfoDb,genome)
+importFrom(GenomeInfoDb,seqinfo)
+importFrom(GenomeInfoDb,seqlengths)
 importFrom(GenomicRanges,"strand<-")
+importFrom(GenomicRanges,end)
 importFrom(GenomicRanges,score)
+importFrom(GenomicRanges,seqnames)
+importFrom(GenomicRanges,start)
 importFrom(GenomicRanges,strand)
 importFrom(Rcpp,evalCpp)
+importFrom(S4Vectors,decode)
 importFrom(rtracklayer,import.bed)
 useDynLib(changchang, .registration = TRUE)

R/exampleTantan.R

@@ -0,0 +1,11 @@
+#' Example tantan data
+#'
+#' Example object loaded from the output of the `tantan -f4` program after
+#' reordering and filterning columns with
+#' `awk 'OFS="\t" {print $1, $2, $3, $6, $5, "."}`
+#'
+#' @format A [`GenomicRanges::GRanges`] object.
+#'
+#' @author Charles Plessy
+#'
+"exampleTantan"

R/telomeres.R

@@ -3,14 +3,17 @@
 #' Searches for telomeric repeats in the whole list of tandem repeats, or
 #' narrowing the search on the ends of sequence features.
 #'
-#' @param gr A [`GenomicRanges::GRanges`] object produced by the [`loadTandems`]
+#' @param gr A [`GenomicRanges::GRanges`] object produced by the [`loadTantan`]
 #'        function
 #' @param motif The telomeric sequence motif, at the end of the plus strand,
 #'        like in TeloBase and the Telomerase Database.
 #' @param narrow Narrow the search on the ends.
 #'
 #' @author Charles Plessy
 #'
+#' @importFrom GenomeInfoDb seqinfo seqinfo<- seqlengths seqlengths<- genome genome<-
+#' @importFrom S4Vectors decode
+#' @importFrom GenomicRanges start end seqnames
 #' @export
 #'
 #' @examples