as_BioData: create a BioData from an other object

In stela2502/BioData: The package allows to annotate a numeric data.table with col and row data

create a BioData from an other object

Description

create a BioData from an other object

Supports sqlite3 databases as used in the cellexalVR application, 10X output files and kallisto out files.

Usage

as_BioData(dat, ...)

## S4 method for signature 'list'
as_BioData(dat)

## S4 method for signature 'matrix'
as_BioData(dat)

## S4 method for signature 'data.frame'
as_BioData(dat)

## S4 method for signature 'cellexalvrR'
as_BioData(dat)

## S4 method for signature 'Seurat'
as_BioData(dat)

## S4 method for signature 'character'
as_BioData(dat, minUMI = 100, minGexpr = NULL)

Arguments

dat	a sqlite database as created by the cellexalvrR::export2cellexalvr() function
...	source object specififc options
minUMI	the minimum UMI count in order to read a cell (default=100)
minGexpr	the minimum UMI count for a gene to be included (default NULL - translates into 1)

Functions

• as_BioData,list-method: create a BioData::R6 object from a Rsubread result list

• as_BioData,matrix-method: convert a matrix to a BioData::R6 object

• as_BioData,data.frame-method: convert a data.frame to a BioData::R6 object

• as_BioData,cellexalvrR-method: convert a cellexalvrR object to a SingleCells::BioData::R6 object

• as_BioData,Seurat-method: convert a seurat object into a SingleCells::BioData::R6 object

• as_BioData,character-method: character path or sqlite3 database name

stela2502/BioData documentation built on Feb. 27, 2025, 6:20 a.m.