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.
GetCTP(
bulk,
cell_types,
markers,
ct_col,
gene_col,
min_gene,
max_gene,
weighted,
w_col,
verbose
)Expression Set containing bulk data
Character vector. Names of cell types.
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.
Character string. Column name specifying cluster/cell type corresponding to each marker gene in markers.
Character string. Column name specifying gene names in markers.
Numeric. Min number of genes to use for each cell type.
Numeric. Max number of genes to use for each cell type.
Boolean. Whether to use weights for gene prioritization
Character string. Column name for weights, such as "avg_logFC", in markers
Boolean. Whether to print log info during decomposition. Errors will be printed regardless.
A List. Slot cors contains list of vectors with correlation coefficients. Slot ctps contains list of CTP objects returned by GetCTP