example/__alt_exec_modes/run.use_zscores.R

#!/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
                             )
broadinstitute/inferCNV documentation built on Jan. 3, 2024, 6:32 p.m.