% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/TENxPeaks-class.R
 \name{TENxPeaks}
 \alias{TENxPeaks}

 \title{Import 10x peak annotation files from 10x}

 \usage{

 TENxPeaks(resource, extension, ...)

 }

 \arguments{
 \item{resource}{character(1) The path to the file}
 

 \item{extension}{character(1) The file extension for the given resource. It
 can usually be obtained from the file path. An override can be provided
 especially for \code{ExperimentHub} resources where the file extension is
 removed.}
 

 \item{...}{Additional inputs to the low level class generator functions}
 }

 \value{

 A \code{GRanges} class object of peak locations

 }

 \description{

 This constructor function is designed to work with the files denoted with
 "peak_annotation" in the file name. These are usually produced as tab
 separated value files, i.e., \code{.tsv}.
 }
 \details{
 The output class allows handling of peak data. It can be used in
 conjunction with the \code{annotation} method on a \code{SingleCellExperiment} to add
 peak information to the experiment. The ranged data is represented as a
 \code{GRanges} class object.

 }
 \examples{
 

 fi <- system.file(
     "extdata", "pbmc_granulocyte_sorted_3k_ex_atac_peak_annotation.tsv",
     package = "TENxIO", mustWork = TRUE
 )

 peak_file <- TENxPeaks(fi)

 peak_anno <- import(peak_file)

 peak_anno

 example(TENxH5)
 
 ## Add peaks to an existing SCE
 ## First, import the SCE from an example H5 file
 h5f <- system.file(
     "extdata", "pbmc_granulocyte_ff_bc_ex.h5",
     package = "TENxIO", mustWork = TRUE
 )
 con <- TENxH5(h5f)

 sce <- import(con)

 ## auto-import peaks when using annotation<-

 annotation(sce, name = "peak_annotation") <- peak_file

 annotation(sce)

 }