ERCCSpikeInConcentrations: Obtain ERCC concentrations

In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

Obtain ERCC concentrations

Description

Obtain ERCC spike-in concentrations from the Thermo Fisher Scientific website.

Usage

ERCCSpikeInConcentrations(
  volume = NULL,
  dilution = NULL,
  mix = c("1", "2"),
  legacy = FALSE
)

Arguments

volume	Numeric scalar specifying the added volume (in nanoliters) of ERCC spike-in mixture. Only used if dilution is specified.
dilution	Numeric scalar specifying the dilution factor used for the added volume of the spike-in mixture. Only used if volume is specified.
mix	String specifying whether to compute the number of molecules for mix 1 or 2. Only used if both dilution and volume are specified.
legacy	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

Details

If volume and dilution are specified, an additional column is added to the output specifying the number of molecules of spike-in transcipt for the specified mix.

All data are downloaded from ExperimentHub and cached for local re-use. Specific resources can be retrieved by searching for scRNAseq/ercc-concentrations.

Value

A DataFrame object with one row per ERCC spike-in transcript. This contains information such as the spike-in concentration in each mix.

Author(s)

Alan O'Callaghan

Examples

df <- ERCCSpikeInConcentrations()

LTLA/scRNAseq documentation built on April 24, 2024, 5:58 p.m.