#!/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.no_spike"
# perform infercnv operations to reveal cnv signal
infercnv_obj = infercnv::run(infercnv_obj,
cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
out_dir=out_dir,
cluster_by_groups=T,
plot_steps=F,
include.spike=F # used for final scaling to fit range (0,2) centered at 1.
)
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