findRefinx {TOAST} | R Documentation

## findRefinx

### Description

Find index for marker genes with largest coefficient of variation based on raw data.

### Usage

    findRefinx(rawdata, nmarker=1000, sortBy = "var")

### Arguments

`rawdata` | A data matrix with rows representing features and columns represeting samples; or a SummarizedExperiment object.
`nmarker` | Desired number of markers after selection. Default is 1000.
`sortBy` | Desired method to select features. "var" represents selecting by largest variance. "cv" represents selecting by largest coefficients of variation. Default is "var".

### Value

A vector of index for the selected markers.

### Author(s)

Ziyi Li <ziyi.li@emory.edu>

### References

Ziyi Li, Zhijin Wu, Peng Jin, Hao Wu. "Dissecting differential signals in high-throughput data from complex tissues."

### Examples

    Y_raw <- matrix(runif(5000*20, 0, 1), 5000, 20)
    idx <- findRefinx(Y_raw, nmarker=500)
    idx2 <- findRefinx(Y_raw, nmarker=500, sortBy = "cv")

[Package TOAST version 1.1.2 Index]