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.
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
Slots in the infercnv object include: