filterHighPNormals: filterHighPNormals: Filter the HMM identified CNV's by the...

In broadinstitute/infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data

filterHighPNormals: Filter the HMM identified CNV's by the CNV's posterior probability of belonging to a normal state.

Description

The following function will filter the HMM identified CNV's by the CNV's posterior probability of belonging to a normal state identified by the function inferCNVBayesNet(). Will filter CNV's based on a user desired threshold probability. Any CNV with a probability of being normal above the threshold will be removed.

Usage

filterHighPNormals(MCMC_inferCNV_obj, HMM_states, BayesMaxPNormal, useRaster)

Arguments

MCMC_inferCNV_obj	MCMC infernCNV object.
HMM_states	InferCNV object with HMM states in expression data.
BayesMaxPNormal	Option to filter CNV or cell lines by some probability threshold.
useRaster	Option to use rasterization when plotting

Value

Returns a list of (MCMC_inferCNV_obj, HMM_states) With removed CNV's.

Examples

data(mcmc_obj)

mcmc_obj_hmm_states_list <- infercnv::filterHighPNormals( MCMC_inferCNV_obj = mcmc_obj, 
                                          HMM_states        = HMM_states, 
                                          BayesMaxPNormal   = 0.5)

broadinstitute/infercnv documentation built on Dec. 3, 2023, 6:58 p.m.