infercnv-class: The infercnv Class

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

The infercnv Class

Description

An infercnv object encapsulates the expression data and gene chromosome ordering information that is leveraged by infercnv for data exploration. The infercnv object is passed among the infercnv data processing and plotting routines.

Details

Slots in the infercnv object include:

Slots

expr.data

<matrix> the count or expression data matrix, manipulated throughout infercnv ops

count.data

<matrix> retains the original count data, but shrinks along with expr.data when genes are removed.

gene_order

<data.frame> chromosomal gene order

reference_grouped_cell_indices

<list> mapping [['group_name']] to c(cell column indices) for reference (normal) cells

observation_grouped_cell_indices

<list> mapping [['group_name']] to c(cell column indices) for observation (tumor) cells

tumor_subclusters

<list> stores subclustering of tumors if requested

options

<list> stores the options relevant to the analysis in itself (in contrast with options relevant to plotting or paths)

.hspike

a hidden infercnv object populated with simulated spiked-in data

broadinstitute/infercnv documentation built on Nov. 19, 2024, 1:30 a.m.