sample-scripts/make_accessibility_matrix.R

In FabianErdel/RWire: Identification of co-regulated genomic regions based on correlation analysis

# make tiles for chromosome 1 (using default tile size)
tiles <- makeTiles(1)

# make accessibility matrix
am <- makeAccMatrix("your_path", tiles)

# save accessibility matrix
write.table(am@accmat, file = "your_path2", sep = "\t", row.names = FALSE, quote = FALSE)

# make histogram for integrations per cell and integrations per region
hist_ipc <- makeIPCHist(am)
print(hist_ipc)

hist_ipr <- makeIPRHist(am)
print(hist_ipr[[1]])

# print stats
makeIPCStats(am)
makeIPRStats(am)