HoneyBADGER-class: A Reference Class to represent single-cell RNA-seq data for...

In JEFworks/HoneyBADGER: HMM-integrated Bayesian approach for detecting CNV and LOH events using single-cell RNA-seq data

Description

A Reference Class to represent single-cell RNA-seq data for HoneyBADGER analysis

Fields

r

single cell alternative allele count matrix

n.sc

single cell snp coverage matrix

l

bulk alternative allele count vector

n.bulk

bulk snp coverage vector

r.maf

single cell lesser allele count matrix

l.maf

bulk lesser allele count vector

gexp.sc

gene expression matrix

gexp.ref

reference gene expression matrix

gexp.norm

normalized gene expression matrix

mvFit

estimated expression magnitude variance as a function of number of genes

dev

expected absolute gene expression deviance due to CNV

snps

GenomicRanges representation of snps in r

genes

GenomicRanges representation of gene positions for genes in gexp.sc

geneFactor

mapping of snps to genes

pred.snps.r

matrix of cells and snps affected by cnv

pred.genes.r

matrix of cells and snps affected by cnv

bound.snps.old

temporary list of snps within cnv region used during recursion

bound.snps.final

list of snps within cnv region

bound.genes.old

temporary list of snps within cnv region used during recursion

bound.genes.final

list of snps within cnv region

results

retested posterior probabilities

summary

summary of posterior probabilities

cnvs

GenomicRanges of identified CNVs

JEFworks/HoneyBADGER documentation built on July 24, 2021, 3:01 p.m.