R package for evaluating the performance of microarray data normalization and batch effects correction in tumor subtyping using microRNA data.
Before installing the PRECISION.array.subtyping
package, users should have installed R
with version 3.5.0 or higher.
Users should install the following packages prior to installing PRECISION.array.subtyping
, from an R
session:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sva")
BiocManager::install("vsn")
From an R
session, type:
require(devtools)
install_github("LXQin/PRECISION.array.subtyping")
Please check the user's guide for the detailed instructions on how to use the functions in the package. You may also run the following code in the R
session:
library(PRECISION.array.subtyping)
data("example_data", package = "PRECISION.array.subtyping")
uni_true_cluster = rep(NA,dim(example_data)[2])
uni_true_cluster[which(substr(colnames(example_data),7,7)=="E")] = 1
uni_true_cluster[which(substr(colnames(example_data),7,7)=="V")] = 2
results = cluster_other(dat = example_data, true_cluster = uni_true_cluster,
clust_method = "kmeans")
str(results)