CIMseqMultiplets: CIMseqMultiplets

In EngeLab/CIMseq: CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method

Description

Subtitle

Usage

## S4 method for signature 'CIMseqMultiplets'
getData(x, n = NULL)

## S4 replacement method for signature 'CIMseqMultiplets'
getData(x, n = NULL) <- value

## S4 method for signature 'CIMseqMultiplets'
c(x, ...)

CIMseqMultiplets(counts, ...)

## S4 method for signature 'missing'
CIMseqMultiplets(counts, ...)

## S4 method for signature 'matrix'
CIMseqMultiplets(
  counts,
  counts.ercc = matrix(nrow = 0, ncol = 0),
  features,
  norm.to = 1e+06,
  ...
)

## S4 method for signature 'CIMseqMultiplets'
initialize(.Object, ..., counts, counts.log, counts.cpm, counts.ercc, features)

## S4 method for signature 'CIMseqMultiplets'
show(object)

Arguments

x	CIMseqMultiplets; CIMseqMultiplets object.
n	Data to extract from CIMseqMultiplets object.
value	Replacment value.
...	additional arguments to pass on
counts	matrix; Counts matrix with samples as columns and genes as rows.
counts.ercc	matrix; A matrix containing ercc spike-in reads.
features	numeric; The indexes of the features/genes for use in deconvolution.
.Object	Internal object.
counts.log	matrix; Log2 normalized counts per million.
counts.cpm	matrix; Normalized counts per million.
object	CIMseqMultiplets; A CIMseqMultiplets to show.

Details

Imports count, count.ercc, and feature data to a CIMseqSinglets object for sequenced multiplets.

Value

CIMseqMultiplets object.

Author(s)

Jason T. Serviss

Examples

s <- grepl("^s", colnames(testCounts))
ercc <- grepl("^ERCC\\-[0-9]*$", rownames(testCounts))
features <- selectTopMax(testCounts[!ercc, s], 2000)
cObj <- CIMseqMultiplets(testCounts[!ercc, !s], testCounts[ercc, !s], features)

EngeLab/CIMseq documentation built on Jan. 25, 2022, 5 a.m.