De noising Filters

inferCNV de-noising filters

These de-noising filter options are available for manipulating the residual expression intensities with the goal of reducing the noise (residual signal in the normal cells) while retaining the signal in tumor cells that could be interpreted as supporting CNV.

The residual normal signal is derived from the preliminary inferCNV object, which has been smoothed, centered, and the mean of the normal (reference) cells subtracted:

Filtering using defined thresholds:

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,
                             denoise=T,
                             noise_filter=0.1   ## hard thresholds
                             )