#!/usr/bin/env Rscript
library("infercnv")
# create the infercnv object
infercnv_obj = CreateInfercnvObject(raw_counts_matrix="../oligodendroglioma_expression_downsampled.counts.matrix",
annotations_file="../oligodendroglioma_annotations_downsampled.txt",
delim="\t",
gene_order_file="../gencode_downsampled.txt",
ref_group_names=c("Microglia/Macrophage","Oligodendrocytes (non-malignant)"))
out_dir="output_dir_use_zscores"
# perform infercnv operations to reveal cnv signal
infercnv_obj = infercnv::run(infercnv_obj,
cutoff=1,
out_dir=out_dir,
cluster_by_groups=T,
plot_steps=T,
use_zscores=T,
include.spike=T
)
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