TENxPeaks-class: TENxPeaks: The class to represent 10x Peaks files

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

TENxPeaks: The class to represent 10x Peaks files

Description

This class 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

## S4 method for signature 'TENxPeaks,ANY,ANY'
import(con, format, text, ...)

## S4 replacement method for signature 'SingleCellExperiment,ANY'
annotation(object, ...) <- value

## S4 method for signature 'SingleCellExperiment'
annotation(object, ...)

Arguments

con	The connection from which data is loaded or to which data is saved. If this is a character vector, it is assumed to be a file name and a corresponding file connection is created and then closed after exporting the object. If it is a BiocFile derivative, the data is loaded from or saved to the underlying resource. If missing, the function will return the output as a character vector, rather than writing to a connection.
format	The format of the output. If missing and con is a file name, the format is derived from the file extension. This argument is unnecessary when con is a derivative of BiocFile.
text	If con is missing, this can be a character vector directly providing the string data to import.
...	Parameters to pass to the format-specific method.
object	The object to export.
value	The annotation information to set on object.

Details

This class is a straightforward class for handling 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 TENxPeaks class object

Functions

• import(con = TENxPeaks, format = ANY, text = ANY): Import a peaks_annotation file from 10x as a GRanges representation

• annotation(object = SingleCellExperiment) <- value: Replacement method to add annotation data to a SingleCellExperiment

• annotation(SingleCellExperiment): Extraction method to obtain annotation data from a SingleCellExperiment representation

LiNk-NY/TENxIO documentation built on Dec. 6, 2024, 8:38 a.m.