help files

man/GFF_att.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/GFF_att.R
+\name{GFF_att}
+\alias{GFF_att}
+\title{Extract attributes from gff.}
+\usage{
+GFF_att(..., att.list = c("GeneID", "Name", "gene"))
+}
+\value{
+a \code{\link[data.table]{data.table}}.
+}
+\description{
+Extract attributes from gff file  \code{\link[data.table]{data.table}}.
+}
+\details{
+This internal function is use by \code{\link{build_genome_features}} in order to extract attributes from gff
+and return a  \code{\link[data.table]{data.table}}.
+}
+\keyword{internal}

man/Plot.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Plot.R
+\name{Plot}
+\alias{Plot}
+\title{Plot overlapped_genome_features graphs.}
+\usage{
+Plot(object, type)
+}
+\arguments{
+\item{object}{an \code{\link{overlapped_genome_features-class}} object.}
+
+\item{type}{a \code{\link[base]{character}} which coulde be "bar" or "line".}
+}
+\value{
+a \code{\link[plotly]{plot_ly}} object.
+}
+\description{
+Plot overlapped_genome_features graphs bar or line.
+}
+\details{
+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.
+}
+\examples{
+###################
+ # display bar plot
+GenomeFeatures::Plot(features_overlaps,"bar")
+
+###################
+ # display bar plot
+GenomeFeatures::Plot(features_overlaps,"line")
+}

man/Table.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/Table.R
+\name{Table}
+\alias{Table}
+\title{extract the annotation table.}
+\usage{
+Table(object)
+}
+\arguments{
+\item{object}{an \code{\link{overlapped_genome_features-class}} object.}
+}
+\value{
+a \code{\link[data.table]{data.table}} object.
+}
+\description{
+extract the annotation table from an \code{\link{overlapped_genome_features-class}} object.
+}
+\details{
+This method is a simple accessor to the stored genomic coordinates annnotation \code{\link[data.table]{data.table}}
+from an \code{\link{overlapped_genome_features-class}} object.
+}
+\examples{
+###################
+annot<-GenomeFeatures::Table(features_overlaps)
+}

man/build_genome_features.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/build_genome_features.R
+\name{build_genome_features}
+\alias{build_genome_features}
+\title{build a convenient genomic features object.}
+\usage{
+build_genome_features(txdb, features = base::c("promoter", "UTR5",
+  "UTR3", "exon", "intron", "cds", "downstream"),
+  parameters = base::list(promoter_ranges = base::list(upstream = 3000,
+  downstream = 500), downstream_range = 1000))
+}
+\arguments{
+\item{txdb}{a txdb database built with \pkg{GenomicFeatures} (see example).}
+
+\item{features}{a \code{\link[base]{vector}} of features \code{\link[base]{character}} with by
+default all the availables features ("promoter", "UTR5", "UTR3", "exon", "intron", "cds", and "downstream").}
+
+\item{parameters}{a \code{\link[base]{list}} of parameters to use in order to define promoter and
+downstream ranges distance to TSS (Transcript Start Site) or TES (Transcript End Site).
+\itemize{
+ \item{promoter_ranges: a \code{\link[base]{list}} with upstream and dowstream  elements distance (in base) to TSS}.
+ \item{downstream_range: the dowstream distance (in base) to the TES}.
+}}
+}
+\value{
+a \code{\link{genome_features-class}} object.
+}
+\description{
+build a convenient \code{\link{genome_features-class}} object needed for find overlaps beetween
+selected features and genomic coordinates in a single step.
+}
+\details{
+This method build a convenient \code{\link{genomic_features-class}} object, in order to be used for finding overlaps beetween
+all selected features and genomic coordinates with the \code{\link{genome_features_overlaps}} method.
+}
+\examples{
+
+###################
+utils::download.file("ftp://ftp.ncbi.nlm.nih.gov/genomes/Gallus_gallus/GFF/ref_Gallus_gallus-5.0_top_level.gff3.gz",
+quiet=T,destfile = "galGal5_gff.gz")
+
+##################
+#  uncompress the file
+R.utils::gunzip("galGal5_gff.gz")
+
+###################
+# build the database
+toplevel=GenomicFeatures::makeTxDbFromGFF(
+ file="galGal5_gff",
+ format="gff",
+ organism="Gallus gallus",
+ taxonomyId=9031,
+ dbxrefTag="ID"
+)
+
+###################
+# build genome_features object from txdb
+features<-GenomeFeatures::build_genome_features(
+ toplevel,
+ features=base::c("promoter","UTR5","UTR3","exon","intron","cds","downstream"),
+ parameters = base::list(
+   promoter_ranges=base::list(
+     upstream=3000,
+     downstream=500
+   ),
+   downstream_range=1000
+ )
+)
+}

man/genome_features-class.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/genome_features.R
+\docType{class}
+\name{genome_features-class}
+\alias{genome_features-class}
+\title{genome_features class object definition.}
+\description{
+This class is invoked by \code{\link{build_genome_features}} method in order to store for each features
+a \code{\link[base]{list}} with \code{\link[GenomicRanges]{GRanges}} and \code{\link[data.table]{data.table}} elements.
+}
+\section{Slots}{
+
+\describe{
+\item{\code{metadata}}{a \code{\link[base]{list}} with provided txdb \code{\link[AnnotationDbi]{metadata}}.}
+
+\item{\code{promoter}}{a \code{\link[base]{list}} with \code{\link[GenomicRanges]{GRanges}} and \code{\link[data.table]{data.table}} elements.}
+
+\item{\code{UTR5}}{a \code{\link[base]{list}} with \code{\link[GenomicRanges]{GRanges}} and \code{\link[data.table]{data.table}} elements.}
+
+\item{\code{exon}}{a \code{\link[base]{list}} with \code{\link[GenomicRanges]{GRanges}} and \code{\link[data.table]{data.table}} elements.}
+
+\item{\code{intron}}{a \code{\link[base]{list}} with \code{\link[GenomicRanges]{GRanges}} and \code{\link[data.table]{data.table}} elements.}
+
+\item{\code{cds}}{a \code{\link[base]{list}} with \code{\link[GenomicRanges]{GRanges}} and \code{\link[data.table]{data.table}} elements.}
+
+\item{\code{UTR3}}{a \code{\link[base]{list}} with \code{\link[GenomicRanges]{GRanges}} and \code{\link[data.table]{data.table}} elements.}
+
+\item{\code{downstream}}{a \code{\link[base]{list}} with \code{\link[GenomicRanges]{GRanges}} and \code{\link[data.table]{data.table}} elements.}
+
+\item{\code{gff}}{a \code{\link[data.table]{data.table}} with the gff.}
+}}
+

man/genome_features_overlaps.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/genome_features_overlaps.R
+\name{genome_features_overlaps}
+\alias{genome_features_overlaps}
+\title{find overlaps between genomic coordinates and features.}
+\usage{
+genome_features_overlaps(peaks, features, figs_path = "./data/figs/",
+  ignore.strand = T)
+}
+\arguments{
+\item{peaks}{a  \code{\link[base]{list}} of \code{\link[GenomicRanges]{GRanges}} objects elements provided by \code{\link{readPeakFile}}.}
+
+\item{features}{a \code{\link[base]{vector}} of features \code{\link[base]{character}} with by
+default all tha availables features ("promoter", "UTR5", "UTR3", "exon", "intron", "cds", and "downstream").}
+
+\item{figs_path}{the path where print the \code{\link[UpSetR]{upstet}} plots. ("./data/figs/", by default).}
+
+\item{ignore.strand}{ignore peak coordinate orientation (defaul to TRUE).}
+}
+\value{
+an \code{\link{overlapped_genome_features-class}} object.
+}
+\description{
+find overlaps between genomic coordinates and features, and store results in an \code{\link{overlapped_genome_features-class}} object.
+}
+\details{
+This method build a convenient genomic features object, in order to be used for finding overlaps beetween
+all needed features and peaks coordinates with \code{\link{genome_features_overlaps}}.
+}
+\examples{
+###################
+features_overlaps<-GenomeFeatures::genome_features_overlaps(
+ peaks,
+ features,
+ figs_path="./data/output/",
+ ignore.strand = T
+)
+}

man/overlapped_genome_features-class.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/overlapped_genome_features.R
+\docType{class}
+\name{overlapped_genome_features-class}
+\alias{overlapped_genome_features-class}
+\title{overlapped_genome_features class object definition.}
+\description{
+This class is invoked by \code{\link{genome_features_overlaps}} method in order to store
+the genomic coordinates annotation \code{\link[data.table]{data.table}}, and features distribution
+\code{\link[data.table]{data.table}} and \code{\link[plotly]{plot_ly}}.
+}
+\section{Slots}{
+
+\describe{
+\item{\code{annotation}}{a  \code{\link[data.table]{data.table}}.}
+
+\item{\code{distribution}}{a \code{\link[base]{list}} with \code{\link[data.table]{data.table}} and \code{\link[plotly]{plot_ly}}  elements.}
+}}
+

man/readPeakFile.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/readPeakFile.R
+\name{readPeakFile}
+\alias{readPeakFile}
+\title{Read peakfile}
+\usage{
+readPeakFile(file)
+}
+\arguments{
+\item{file}{peak file path.}
+}
+\value{
+a \code{\link[GenomicRanges]{GRanges}} object.
+}
+\description{
+This function is use to  read peaks file, also known bed file, with genomic coordinates (chr, start, end, strand),
+and to convert it in \code{\link[GenomicRanges]{GRanges}} object.
+}
+\details{
+This function read peaks coordinates file (bed file) and store the results in a \code{\link[GenomicRanges]{GRanges}} object.
+}
+\examples{
+###################
+# read peak file (package sample from NCBI)
+peaks<-GenomeFeatures::readPeakFile(
+ base::system.file(
+  "extdata/data/input/NCBI_sample.bed",
+  package="GenomeFeatures"
+ )
+)
+}