I’m working with matched single cell data, where we have treated and untreated samples for the same patient. I ran CNV analysis using the infercnv
package.
I’ve followed the tutorial:
# data matrix
counts_matrix <- scData@assays$RNA@counts
meta = data.frame(labels = Idents(scData), row.names = names(Idents(scData)))
unique(meta$labels) # check the cell labels
# Create the infercnv object
infercnv_obj <- CreateInfercnvObject(raw_counts_matrix = counts_matrix,
annotations_file = meta,
delim = "\t",
gene_order_file = "hg38_gencode_v27.txt",
ref_group_names = NULL)
# perform infercnv operations to reveal cnv signal
infercnv_obj = infercnv::run(infercnv_obj,
cutoff=1, # use 1 for smart-seq, 0.1 for 10x-genomics
out_dir="output_dir", # dir is auto-created for storing outputs
cluster_by_groups=T, # cluster
denoise=T,
HMM=T
)
Now, I’m not sure how to plot the results. Any help would be appreciated.
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