findIndex: findIndex

In scDD: Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

Description

Find a reasonable set of genes (one mode and at least 25 to use for simulation.

Usage

findIndex(SCdat, condition = "condition")

Arguments

SCdat

An object of class SingleCellExperiment that contains normalized single-cell expression and metadata. The assays slot contains a named list of matrices, where the normalized counts are housed in the one named normcounts. This matrix should have one row for each gene and one sample for each column. The colData slot should contain a data.frame with one row per sample and columns that contain metadata for each sample. This data.frame should contain a variable that represents biological condition, which is in the form of numeric values (either 1 or 2) that indicates which condition each sample belongs to (in the same order as the columns of normcounts). Optional additional metadata about each cell can also be contained in this data.frame, and additional information about the experiment can be contained in the metadata slot as a list.

condition

A character object that contains the name of the column in colData that represents the biological group or condition of interest (e.g. treatment versus control). Note that this variable should only contain two possible values since scDD can currently only handle two-group comparisons. The default option assumes that there is a column named "condition" that contains this variable.

Value

Vector of indices for a reasonable set of genes that can be used for simulation.

References

Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, Kendziorski C. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology. 2016 Oct 25;17(1):222. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1077-y

scDD documentation built on Nov. 8, 2020, 7:10 p.m.