Commit deda7bb2 authored by Aurelien Brionne's avatar Aurelien Brionne
Browse files

vignette update

parent 6e280a7d
......@@ -6,6 +6,7 @@ exportMethods(Plot)
exportMethods(Table)
exportMethods(build_genome_features)
exportMethods(genome_features_overlaps)
import(S4Vectors)
importFrom(AnnotationDbi,as.data.frame)
importFrom(AnnotationDbi,keys)
importFrom(AnnotationDbi,metadata)
......
#' @title build a convenient genomic features object.
#' @description build a convenient \code{\link{genome_features-class}} object needed for find overlaps beetween
#' @description build a convenient \code{\link{genome_features-class}} object needed for find overlaps between
#' selected features and genomic coordinates in a single step.
#' @importFrom AnnotationDbi select keys as.data.frame metadata
#' @importFrom GenomicFeatures promoters transcripts fiveUTRsByTranscript threeUTRsByTranscript exonsBy intronsByTranscript cdsBy
#' @importFrom S4Vectors mcols
#' @import S4Vectors
#' @importFrom GenomicRanges flank
#' @importFrom rtracklayer import
#' @importFrom BiocGenerics as.data.frame
......
......@@ -38,7 +38,7 @@ downstream ranges distance to TSS (Transcript Start Site) or TES (Transcript End
a \code{\link{genome_features-class}} object.
}
\description{
build a convenient \code{\link{genome_features-class}} object needed for find overlaps beetween
build a convenient \code{\link{genome_features-class}} object needed for find overlaps between
selected features and genomic coordinates in a single step.
}
\details{
......
......@@ -91,7 +91,6 @@ toplevel=GenomicFeatures::makeTxDbFromGFF(
Now, we build a convenient object with `GenomeFeatures::build_genome_features`, needed for find overlaps beetween all selected features and genomic coordinates targets into a single step (see below).
```{r features}
library(S4Vectors)
# build genome features
features<-build_genome_features(
toplevel,
......
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