estimateCells: estimateCells

In jasonserviss/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 'CIMseqSinglets'
estimateCells(singlets, multiplets,
  theoretical.max = Inf, warning = TRUE, ...)

Arguments

singlets	A CIMseqSinglets object.
multiplets	A CIMseqMultiplets object.
theoretical.max	integer; Cuts the estimated cell number at the provided value such that all values > than the theoretical.max become equal to the theoretical.max.
warning	logical; Indicates if a warning should be issued when all ERCC counts for a sample are equal to 0. If this warning is issued it can be resolved by setting the ERCC reads for these samples to NA.
...	additional arguments to pass on

Details

Uses ERCC data to calculate the fraction of ERCC reads in the samples. In addition, this function utilizes ERCC data to estimate the cell number in each sample.

Value

A data frame including the fraction of ercc reads and cell counts for each sample.

Author(s)

Jason T. Serviss

Examples

output <- estimateCells(CIMseqSinglets_test, CIMseqMultiplets_test)

jasonserviss/CIMseq documentation built on Jan. 11, 2020, 4:42 a.m.