@@ -25,11 +25,11 @@ Plot overlapped_genome_features graphs bar or line.
This method is a simple accessor to the stored \code{\link[plotly]{plot_ly}} bar or line plots from the \code{\link{overlapped_genome_features-class}} object.
@@ -38,24 +36,23 @@ In this vignette, we use only the chicken (galGal5) chromosome 1 (NC_006088.4) t
## Load the genomic coordinates targets
At the first step we read peaks files (also known bed files with genomic coordinates chr, start, end, strand) in a `base::list`, and convert it in GRanges object with `GenomeFeatures::readPeakFile`.
At the first step we read peaks files (also known bed files with genomic coordinates chr, start, end, strand) in a `list`, and convert it in GRanges object with `GenomeFeatures::readPeakFile`.
<u>Important note:</u> In this vignette, we use only a part of the chicken (galGal5) chromosome 1 (NC_006088.4) gff to illustrate `GenomeFeatures` results.
```{r TxDb_build}
###################
# build the database
toplevel=GenomicFeatures::makeTxDbFromGFF(
file= base::system.file(
"/extdata/data/input/galGal5.gff",
package="GenomeFeatures"
file= system.file(
"/extdata/data/input/galGal5.gff",
package="GenomeFeatures"
),
format="gff",
organism="Gallus gallus",
taxonomyId=9031,
dbxrefTag="ID"
format="gff",
organism="Gallus gallus",
taxonomyId=9031,
dbxrefTag="ID"
)
```
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).