inst/shiny/www/Smoothing_methods.md

In broadinstitute/infercnvApp: An R shiny app to Infer Copy Number Variation from Single-Cell RNA-Seq Data

Smoothing methods

Each method is applied on individual cells' data, and independently per chromosome.

Runmeans

Simple mean over the genes within (window_size-1)/2 on each side.

Pyramidal smoothing

Weighted mean over the genes within (window_size-1)/2 on each side. With n = (window_size-1)/2, the weight for the m-th gene in the neighborhood of a given gene is (n+1-m)/(n+1)

Coordinates based method

This feature is only available from version 1.1.3 onward. Weighted mean over the genes within window_size base pairs on each side of a given gene. The weight for a gene with their center at m base pairs from the current gene's center is 1-(m/window_size). This method can give the "cleanest" limits for CNVs, when there is a large gap around it among the expressed genes.

broadinstitute/infercnvApp documentation built on Sept. 21, 2021, 4:17 p.m.