SCDC_qc_ONE: Clustering QC for single cells from one subject

In crhisto/SCDC: Bulk RNA-seq deconvolution by scRNA-seq with multi-reference datasets

Description

Clustering QC for single cells from one subject

Usage

SCDC_qc_ONE(
  sc.eset,
  ct.varname,
  sample,
  scsetname = "Single Cell",
  ct.sub,
  iter.max = 1000,
  nu = 1e-04,
  epsilon = 0.01,
  arow = NULL,
  weight.basis = F,
  qcthreshold = 0.7,
  generate.figure = T,
  cbPalette = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2",
    "#D55E00", "#CC79A7"),
  ...
)

Arguments

sc.eset	ExpressionSet object for single cells
ct.varname	variable name for 'cell type'
sample	variable name for subject/sample
scsetname	the name for the single cell dataset
ct.sub	a subset of cell types that are selected to construct basis matrix
iter.max	the maximum number of iteration in WNNLS
nu	a small constant to facilitate the calculation of variance
epsilon	a small constant number used for convergence criteria
arow	annotation of rows for pheatmap
qcthreshold	the probability threshold used to filter out questionable cells
generate.figure	logical. If generate the heatmap by pheatmap or not. default is TRUE.

Value

a list including: 1) a probability matrix for each single cell input; 2) a clustering QCed ExpressionSet object; 3) a heatmap of QC result.

crhisto/SCDC documentation built on Dec. 19, 2021, 6:19 p.m.