findIndex {scDD} | R Documentation

## findIndex

### 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

[Package scDD version 1.4.0 Index]