sCVparams-class: Parameters used in the sCVdata class and methods.

In BaderLab/scClustViz: Differential Expression-based scRNAseq Cluster Assessment and Viewing

Parameters used in the sCVdata class and methods.

Description

An S4 class storing parameters used in the sCVdata class and methods. Access this object from the containing sCVdata object with Param. Slots are accessed using Param(sCVdata,slotName)

Slots

assayType

A character vector representing the assay slot in which the expression data is stored in the input object. For SingleCellExperiment objects, this is often "logcounts". This is not required for Seurat v1 or v2 objects (set to ""). For Seurat v3 objects, this is often "RNA". Optionally, you can specify the Seurat v3 assay slot to use (i.e. "data" or "counts") as the second element of this character vector. For example, assayType = c("SCT","counts"). See getExpr for details.

DRforClust

A length-one character vector representing the dimensionality reduction method used as the input for clustering. This is commonly PCA, and should correspond to the slot name of the cell embedding in your input data - either the type argument in reducedDim(x,type) or the reduction.type argument in GetDimReduction(object,reduction.type) (v2) or reduction in Embeddings(object,reduction).

exponent

A length-one numeric vector representing the base of the log-normalized gene expression data to be processed. Generally gene expression data is transformed into log2 space when normalizing (set this to 2), though Seurat uses the natural log (set this to exp(1)).

pseudocount

A length-one numeric vector representing the pseudocount added to the data during log-normalization to avoid log(0) errors. Generally this is 1.

DRthresh

A length-one numeric vector between 0 and 1 representing the detection rate threshold for inclusion of a gene in the differential expression testing. A gene will be included if it is detected in at least this proportion of cells in at least one of the clusters being compared. Commonly set to 0.1.

See Also

sCVdata for containing class.

BaderLab/scClustViz documentation built on Sept. 10, 2023, 11:51 p.m.