cellTypeAssignMarkerGenes: 'cellTypeAssignMarkerGenes' assigns CDSeq-identified cell...
In CDSeq: A Complete Deconvolution Method using Sequencing Data

View source: R/cellTypeAssignMarkerGenes.R

cellTypeAssignMarkerGenes assigns CDSeq-identified cell types using user-provided marker gene list and plots heatmap.

cellTypeAssignMarkerGenes(
  cell_gep = NULL,
  marker_gene_list = NULL,
  threshold = 2,
  fig_path = getwd(),
  rowlabelsize = 1,
  collabelsize = 1,
  margins = c(3, 0),
  fig_width = 100,
  fig_height = 100,
  keysize = 1,
  srtcol = 45,
  keypar = c(3.5, 0, 3, 0),
  heatmap_name = "cellTypeAssign_heatmap.pdf",
  heatmap_name_fuzzy_assign = "cellTypeAssign_heatmap_fuzzy.pdf",
  verbose = FALSE
)

`cell_gep`	gene expression profile matrix with G rows (genes) and M columns (cell types).
`marker_gene_list`	a G (genes) by C (cell types with known identities) matrix or dataframe that contains the marker genes for each cell type. Column names must be CellType and GeneName.
`threshold`	a numeric value that provides the threshold of whether a known cell type in the marker gene list can be identified.
`fig_path`	the location where the heatmap figure is saved.
`rowlabelsize`	row label size
`collabelsize`	column label size
`margins`	a vector of length 2 indicates row and column label margins
`fig_width`	figure width for pdf figure
`fig_height`	figure height for pdf figure
`keysize`	color key size for heatmap
`srtcol`	column label angle
`keypar`	color key layout
`heatmap_name`	the name of heatmap figure of one-to-one assignment.
`heatmap_name_fuzzy_assign`	the name of heatmap figure of fuzzy assignment.
`verbose`	if TRUE, some information will be printed.

cellTypeAssignMarkerGenes returns a list containing: GEP_markerSum (a A by B matrix where A is nrow(marker_gene_list), B is ncol(cell_gep)),

GEP_markerSum_zscore (row-wise z score of GEP_markerSum),

GEP_matched is cell_gep(,cell_type_idx),

cell_type_idx (column index of cell_gep that are considered matching with cell types in marker_gene_list),

cell_type_matched stores the cell types in marker_gene_list that are considered to be matched with cell_gep,

GEP_markerSum_zscore_matched contains only the rows of GEP_markerSum_zscore that are considered to be matched with some cell types in cell_gep. GEP_markerSum_zscore_matched and GEP_markerSum_zscore have same columns.

cell_type_matched_fuzzy is a zero-one matrix that has the same size as GEP_markerSum_zscore_matched. If (i,j) element is one, means ith cell type in marker_gene_list is assigned to jth element in cell_gep.

CDSeq documentation built on Feb. 10, 2021, 5:07 p.m.