SingleCells: Class interface for single cell data

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

Class interface for single cell data

Description

Class interface for single cell data

Class interface for single cell data

Format

R6Class object.

Value

Object of R6Class to store single cell data.

Super class

BioData::BioData -> SingleCells

Public fields

data

the numerical data as data.frame

samples

the sample annotation as data.frame

annotation

the row annotation as data.frame

usedObj

a multi purpose list to store whichever ananlyis results do not fit in the stats list

stats

all stats with one result for each data row

Active bindings

data

the numerical data as data.frame

samples

the sample annotation as data.frame

annotation

the row annotation as data.frame

usedObj

a multi purpose list to store whichever ananlyis results do not fit in the stats list

stats

all stats with one result for each data row

Methods

Public methods

• SingleCells$force.numeric()

• SingleCells$clone()

Inherited methods

• BioData::BioData$data()

• BioData::BioData$forceAbsoluteUniqueSample()

• BioData::BioData$initialize()

• BioData::BioData$print()

• BioData::BioData$pwd()

• BioData::BioData$rawData()

• BioData::BioData$reorder.genes()

• BioData::BioData$reorder.mds()

• BioData::BioData$reorder.samples()

---

Method force.numeric()

Usage

SingleCells$force.numeric(...)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SingleCells$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

set.seed(1)
dat = matrix(rnorm(1000),ncol=10)
dat = round(dat)
dat = dat - min(dat)
dat = data.frame( dat ) 
colnames(dat) <- paste('Sample', 1:10)
rownames(dat) <- paste( 'gene', 1:100)
samples <- data.frame(SampleID = 1:10, sname = colnames(dat) )
annotation <- data.frame( GeneID = paste( 'gene', 1:100), Start= 101:200 )
x <- SingleCells$new( cbind(annotation,dat), 
  Samples=samples, name="testObject",namecol='sname', outpath = "" )

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