CAEN: Compute the correlation coefficient of gene with category...

In zhangli1109/CAEN: Category encoding method for selecting feature genes for the classification of single-cell RNA-seq

Description

To Compute the correlation coefficient of gene with category number to identify differentially expressed genes.

Usage

CAEN(dataTable, y, K, gene_no_list)

Arguments

dataTable	Matrix or data.frame containing read counts and the row denotes the gene
y	the category for each sample
K	the number of class
gene_no_list	the number of differentially expressed genes you want to select

Value

list(.) A list of computed correlation coefficient and the first some differentially expressed genes , where "r" represents correlation coefficient between gene and category number, and "np" represents the top differential feature label.

Examples

library(SummarizedExperiment)
dat <- newCountDataSet(n=40,p=500,sdsignal=0.1,K=4,param=10,drate=0.4)
x <- t(assay(dat$sim_train_data))                  
y <- as.numeric(colnames(dat$sim_train_data))      
xte <- t(assay(dat$sim_test_data))                 
prob <- estimatep(x=x,y=y,xte=x,beta=1,
type=c("mle","deseq","quantile"),prior=NULL)      
prob0 <- estimatep(x=x,y=y,xte=xte,beta=1,
type=c("mle","deseq","quantile"),prior=NULL)   
myscore <- CAEN(dataTable=assay(dat$sim_train_data),
y=as.numeric(colnames(dat$sim_train_data)),
K=4,gene_no_list=100)

zhangli1109/CAEN documentation built on Nov. 14, 2020, 11:41 a.m.