TENxPeaks: Import 10x peak annotation files from 10x

In LiNk-NY/TENxIO: Import methods for 10X Genomics files

Import 10x peak annotation files from 10x

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., .tsv.

Usage

TENxPeaks(resource, extension, ...)

Arguments

resource	character(1) The path to the file
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 ExperimentHub resources where the file extension is removed.
...	Additional inputs to the low level class generator functions

Details

The output class allows handling of peak data. It can be used in conjunction with the annotation method on a SingleCellExperiment to add peak information to the experiment. The ranged data is represented as a GRanges class object.

Value

A GRanges class object of peak locations

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)

LiNk-NY/TENxIO documentation built on Nov. 16, 2024, 7:10 p.m.