Adjustment of parameter 'leiden_resolution' will change the result of run.final.infercnv_obj@expr.data ?

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Lucas Travil

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Mar 12, 2024, 11:21:58 PMMar 12
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Thank you for developing such a great tool!
Currently, when I perform sample-by-sample CNV calculations, I use a resolution of 0.0001. I wonder if I increase the resolution, which increases the number of subgroups, will it change the final infercnv result? Especially the file run.final.i...@expr.data, I will analyze this file later. These are my codes as follows:
infercnv_obj = infercnv::run(infercnv_obj, cutoff=0.1, # use 1 for smart-seq, 0.1 for 10x-genomics

out_dir="OC_CNV", # dir is auto-created for storing outputs

cluster_by_groups=T, # cluster

denoise=T,

num_threads = 30,

analysis_mode = "subclusters",

leiden_resolution = 0.0001,

output_format = "pdf",

#up_to_step = 15,

HMM=T )

Sincerely,
Lucas

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