CapEff: This function estimates the capture efficiencies of the cells...

In sam-uofl/SwarnSeq: Detection of Differentially Expressed Genes from Single Cell RNA-seq Data

Description

This function estimates the capture efficiencies of the cells from the single-cell RNA-seq studies. It takes input the ERCC spike-in transcript and molecular concentration data, if available or count expression data, if spike-ins are not available.

Usage

CapEff(CountData, CE.range, RNAspike.use, spikes, spike.conc, method)

Arguments

CountData	Observed count data matrix for genes, rows represent genes, columns represent cells.
CE.range	Two-element vector representing the lower and upper limits for the estimated range of capture efficiencies (ONLY needed if RNAspike.use = FALSE, default [0.1, 0.40]).
RNAspike.use	Logical value indicating TRUE/FALSE, if TRUE, spikes and spike.conc information must be provided.
spikes	Observed count matrix for spike-in transcripts, rows represent spike-in transcripts, columns represent cells. Only needed if RNAspike.use = TRUE).
spike.conc	Vector of theoretical count for each spike-in transcript in one cell (ONLY needed if RNAspike.use = TRUE).
method	Character representing the methods to be used for computation of capture efficiencies for cells.

Value

Returns a vector of estimated capture efficiencies for cells given in the scRNA-seq data.

Author(s)

Samarendra Das

sam-uofl/SwarnSeq documentation built on Sept. 6, 2020, 12:09 a.m.