clustering_Kmeans: clustering DEGs by K-means

In jiang-junyao/IReNA: IReNA

clustering DEGs by K-means

Description

This function is used to cluster the DEGs in the expression profile by K-means algorithmn

Usage

clustering_Kmeans(
  RNA1,
  K1 = 1,
  ColumnGroup1 = NULL,
  Scale1 = "row",
  Range1 = c(-Inf, Inf),
  Reorder1 = TRUE,
  RevOrder1 = -1,
  NAcolum1 = NULL
)

Arguments

RNA1	expression profile
K1	numbers of bin
ColumnGroup1	vector, if it is not NULL, this function wil sepate columns according to varible ColumnGroup1, default is NULL
Scale1	character, indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row", "column" and "none"
Range1	numeric, indicating the range of expression values, defalut is c(-Inf, Inf)
Reorder1	logic, indicating whether to order gene through hclustering, defalut is TRUE
RevOrder1	logic, indicating whether to reverser the order
NAcolum1	vector, indicating which columns need to be removed due to NA values

Value

return a data.frame, and the first column is K-means group

Examples

load(system.file("extdata", "test_clustering.rda", package = "IReNA"))
expression_profile = test_clustering[,-1];expression_profile<-na.omit(expression_profile)
clustering_Kmeans(expression_profile, K1=4, Range1=c(-3,3))

jiang-junyao/IReNA documentation built on Nov. 15, 2024, 1:51 a.m.