estimateCellTypeProportions: estimateCellTypeProportions Deconvolution methods for large...

In libcell/deconvBench: A tool for approaches evaluation of cell fraction estimation

estimateCellTypeProportions Deconvolution methods for large functions

Description

estimateCellTypeProportions Deconvolution methods for large functions

Usage

estimateCellTypeProportions(
  method,
  bulkdata,
  signature = NULL,
  scdata = NULL,
  label = NULL,
  celltypenum = NULL,
  tissue = NULL,
  tumortype = NULL,
  reftype = NULL,
  SubMethod = NULL,
  seed = NULL,
  use_docker = FALSE
)

Arguments

method	Select a method from 37 software for estimating the proportion of cellular fractions in mixed samples.they are "Abis","Adapts","Autogenes","Bayice","Bisquerna","Bseqsc", Cdseq_no","Cdseq","Celldistinguisher","Cibersort","Consensustme","Dcq","Debcam","Demixt","Dtangle", "Dtd","Dwls","Enigma","Epic","Estimate","Fardeep","Mcpcounter","Mixture","Momf","Music","Nitumid", "Prede","Quantiseq","Scbiocpm","Scdc","Singscore","Ssgsea","Ticpe","Timer","Toast","Toast_no", Xcell".
bulkdata	A data.frame (nGenes x nSamples) of the genes expression from each bulk sample. This matrix needs to have rownames telling the gene names (corresponds to the gene symbol in the prebuilt reference profiles (e.g. CD8A, MS4A1) It is advised to keep all genes in the bulk instead of a subset of signature genes.
signature	A data frame representing immune cell expression profiles. Each row represents an expression of a gene, and each column represents a different cell type. colnames contains the name of each immune cell type and the rownames includes the genes' symbol. The names of each immune cell type and the symbol of each gene should be unique.
scdata	A data frame with unnormalized data with cells as columns and genes as rows.
label	A cell type label of length equal to the number of columns of the scdata, with each label corresponding to a column of the scdata in turn.
celltypenum	For some reference-free methods, it is necessary to set the number of cell types contained in the mixed sample.
tissue	The tissues of bulk sample, One of "BLOOD","Gedit","LIVER","LUNG","MUSCLE","OVARY","HEART","BONE", "ESOPHAGUS","STOMACH","GASTRIC","PANCREAS","CEREBELLUM", "NEUROTYPES","RETINA","EYE","THYMUS","INTESTINE", "ADRENAL","ESOPHAGEAL","DUODENAL","OLFACTORY","CEREBRUM".
tumortype	23 cancer types from The Cancer Genome Atlas (TCGA).
reftype	defalt is NULL
SubMethod	Subclass methods for cellular component estimation method software. Such as "NNLS".
seed	the random seed
use_docker	Whether to use docker images, TRUE or FALSE.

Value

A data frame of Mixed cellular fractions.

Examples

# Bulk <- Bulk_GSE60424
# SC <- SC_GSE60424
# Label <- Label_GSE60424$Label
# res <-  estimateCellTypeProportions(method = "Music",
#                                    bulkdata = Bulk,
#                                    scdata = SC,
#                                    label = Label,
#                                    SubMethod = "weighted",
                                     use_docker = FALSE)

libcell/deconvBench documentation built on Sept. 24, 2022, 12:36 p.m.