cotMG: Select markers in S matrix with COT

In ChiungTingWu/CAM3: Convex Analysis of Mixtures Version 3

Select markers in S matrix with COT

Description

This function computes cosine values to select markers.

Usage

cotMG(
  data = NULL,
  Sest,
  thres.low = 0.05,
  thres.high = 1,
  cos.thres = 1,
  top = NULL,
  per = NULL
)

Arguments

data	A data set that will be internally coerced into a matrix. If data is not NULL, "thres.low" and "thres.high" would decide which genes should be removed in data. If data is NULL, the thresholds work on "Sest" directly.
Sest	Subpopulation-specific expression matrix. Each row is a gene and each column is a sample.
thres.low	The lower bound of percentage of genes to keep with ranked norm. The value should be between 0 and 1. The default is 0.05.
thres.high	The higher bound of percentage of genes to keep with ranked norm. The value should be between 0 and 1. The default is 1.
cos.thres	The cosine threshold for markers.
top	The upper bound of total markers.
per	The upper bound of markers of each Subpopulation.

Details

This function uses COT to detect markers.

Value

A list of vectors, each of which contains marker genes for one subpopulation.

Examples

data(ratMix3)
data <- ratMix3$X

#Find marker genes
MGlist <- cotMG(data, rASest3$S, cos.thres = 0.99)

ChiungTingWu/CAM3 documentation built on Feb. 14, 2024, 9:22 a.m.