findRefinx: findRefinx

In ziyili20/TOAST: Tools for the analysis of heterogeneous tissues

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 <[e-mail]>

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")

ziyili20/TOAST documentation built on Aug. 28, 2022, 11:28 a.m.