BisqueRNA: GetCTP – R documentation

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GetCTP

Return cell type proportions from bulk

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

BisqueRNA

Decomposition of Bulk Expression with Single-Cell Sequencing

v1.0.4

GPL-3

Authors

Brandon Jew [aut, cre], Marcus Alvarez [aut]

Initial release