BASiCS (version 0.7.30)

BASiCS_D_Data-class: The BASiCS_D_Data class

Description

Container of expression counts from single-cell sequencing experiments in the format required to perform the differential expression and differential over-dispersion tests using BASiCS.

Slots

CountsTest

Matrix of dimensions q times n_test whose elements corresponds to the raw expression counts in the test sample. First q.bio rows correspond to biological genes. Last q-q.bio rows correspond to technical spike-in genes.

CountsRef

Matrix of dimensions q times n_ref whose elements corresponds to the raw expression counts in the reference sample. First q.bio rows correspond to biological genes. Last q-q.bio rows correspond to technical spike-in genes.

Tech

Logical vector of length q. If Tech = F the gene is biological; otherwise the gene is spike-in.

SpikeInputTest

Vector of length q-q.bio whose elements indicate the input number of molecules for the spike-in genes in the test sample (amount per cell).

SpikeInputRef

Vector of length q-q.bio whose elements indicate the input number of molecules for the spike-in genes in the reference sample (amount per cell).

BatchInfoTest

To include batch information in test group (vector of n_test elements)

BatchInfoRef

To include batch information in test group (vector of n_ref elements)

GeneNames

Vector of length q containing gene names. Default value: GeneNames = paste("Gene", 1:q), with numbering order as in the input dataset.

References

Vallejos, Marioni and Richardson (2015). Bayesian Analysis of Single-Cell Sequencing data. PLoS Computational Biology.

Examples

# NOT RUN {
# See vignette

# }