test/01test_c_list.R

In CBIIT-CGBB/scCorr: A graph-based k-partitioning approach for single-cell gene-gene correlation analysis

rm(list=ls());

library(scCorr);

## get data
## 5 clusters of CD4 T cells
ct.c   <- c(6:10); 
## tsne result/output
tsnef  <- "https://github.com/CBIIT-CGBB/scCorr/raw/master/data/01/do_tsne30_2000.txt";
tsne   <- read.table(tsnef, header=T);

## cluster matrix
cluf   <- "https://github.com/CBIIT-CGBB/scCorr/raw/master/data/01/03clust_table.txt";
clu    <- read.table(cluf, header=T, sep="\t");
## check row.names
sum(row.names(tsne)==row.names(clu))==nrow(clu);
## sample index of CD4 T cells in the cluster matrix
s.i    <- which(clu[,23] %in% ct.c);
## some single cells of CD4 T cells 
dat    <- tsne[s.i,];

out           <- c_list(dat, 40);
out.index     <- out[[1]];
out.cellname  <- out[[2]];