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 class 'TENxPeaks,ANY,ANY'
import(con, format, text, ...)
# S4 method for class 'SingleCellExperiment,ANY'
annotation(object, ...) <- value
# S4 method for class 'SingleCellExperiment'
annotation(object, ...)Arguments
- con
The connection from which data is loaded or to which data is saved. If this is a
charactervector, 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
conis a file name, the format is derived from the file extension. This argument is unnecessary whenconis a derivative of BiocFile.- text
If
conis 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.
Functions
import(con = TENxPeaks, format = ANY, text = ANY): Import a peaks_annotation file from 10x as aGRangesrepresentationannotation(object = SingleCellExperiment) <- value: Replacement method to add annotation data to aSingleCellExperimentannotation(SingleCellExperiment): Extraction method to obtain annotation data from aSingleCellExperimentrepresentation