TENxFragments-class: TENxFragments: A class to represent fragments data as...

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

TENxFragments: A class to represent fragments data as GRanges

Description

This class is designed to work mainly with fragments.tsv.gz files from 10x pipelines.

Usage

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

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.

Details

Fragments data from 10x can be quite large. In order to speed up the initial exploration of the data, we use a default of 200 records for loading. Users can change this default value by specifying a new one via the yieldSize argument in the constructor function.

Value

A TENxFragments class object

Methods (by generic)

• import(con = TENxFragments, format = ANY, text = ANY): Import method for representing fragments.tsv.gz data from 10x via Rsamtools and RaggedExperiment

Slots

which

GRanges() A GRanges indicating the regions of interest. This get sent to RSamtools as the param input.

yieldSize

numeric() The number of records to read by default, 200 records will be imported. A warning will be emitted if not modified.

LiNk-NY/TENxIO documentation built on May 3, 2024, 11:08 p.m.