getOccupancyGenome.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/implementation-genome.R
\name{getOccupancyGenome}
\alias{getOccupancyGenome}
\title{Compute Read Occupancy on the Genome}
\usage{
getOccupancyGenome(
  bam_file = NULL,
  gene_name = NULL,
  features = NULL,
  total_reads = NULL,
  assignment_mode = NULL,
  coordinate_to_trans = FALSE,
  return_all_position = FALSE
)
}
\arguments{
\item{bam_file}{Character. Path to the BAM file.}

\item{gene_name}{Character. The gene name for which read occupancy is extracted.}

\item{features}{A \code{data.frame} or \code{GRanges} object containing transcript annotation.}

\item{total_reads}{Numeric. The total number of mapped reads (for RPM normalization).}

\item{assignment_mode}{Character. Specifies the read assignment strategy: \code{"end5"} (5' end) or \code{"end3"} (3' end).}

\item{coordinate_to_trans}{Logical. Whether to convert genomic coordinates to transcript
coordinates. Default is FALSE.}

\item{return_all_position}{Logical; if \code{TRUE}, extracts data for \strong{all mapped regions},
not just the specified gene (default: \code{FALSE}).}
}
\value{
A \code{data.frame} with read occupancy information:
\itemize{
\item \code{rname}: Transcript and gene identifier (\code{"transcript_id|gene_name"}).
\item \code{pos}: Transcriptomic read position.
\item \code{count}: Number of reads at the position.
\item \code{rpm}: Reads per million (RPM) normalized occupancy.
}
}
\description{
The \code{getOccupancyGenome()} function extracts read positions from a BAM file
for a given gene, converts them to transcriptome positions, and calculates
normalized read occupancy (RPM).
}
\examples{
\dontrun{
bam_file <- "example.bam"
gene <- "TP53"
total_mapped_reads <- 1e7
features <- prepareTransInfo_forGenome(gtf_file = "example.gtf")

occupancy_data <- getOccupancyGenome(
  bam_file = bam_file,
  gene_name = gene,
  features = features,
  total_reads = total_mapped_reads
)
head(occupancy_data)
}

}