GetCTP: Return cell type proportions from bulk

In cozygene/bisque: Decomposition of Bulk Expression with Single-Cell Sequencing

Description

Calculate cell type proportions from a data frame containing bulk expression values. Uses PCA (weighted or regular) to estimate relative proportions within each cell type.

Usage

GetCTP(
  bulk,
  cell_types,
  markers,
  ct_col,
  gene_col,
  min_gene,
  max_gene,
  weighted,
  w_col,
  verbose
)

Arguments

bulk	Expression Set containing bulk data
cell_types	Character vector. Names of cell types.
markers	Data frame with columns specifying cluster and gene, and optionally a column for weights, typically the fold-change of the gene. Important that the genes for each cell type are row-sorted by signficance.
ct_col	Character string. Column name specifying cluster/cell type corresponding to each marker gene in markers.
gene_col	Character string. Column name specifying gene names in markers.
min_gene	Numeric. Min number of genes to use for each cell type.
max_gene	Numeric. Max number of genes to use for each cell type.
weighted	Boolean. Whether to use weights for gene prioritization
w_col	Character string. Column name for weights, such as "avg_logFC", in markers
verbose	Boolean. Whether to print log info during decomposition. Errors will be printed regardless.

Value

A List. Slot cors contains list of vectors with correlation coefficients. Slot ctps contains list of CTP objects returned by GetCTP

cozygene/bisque documentation built on May 28, 2021, 7:57 p.m.