scReplicate {scMerge} | R Documentation |
Create replicate matrix for scMerge algorithm using un-/semi-/supervised approaches.
scReplicate(sce_combine, batch = NULL, kmeansK = NULL, exprs = "logcounts", hvg_exprs = "counts", marker = NULL, marker_list = NULL, replicate_prop = 1, cell_type = NULL, cell_type_match = FALSE, cell_type_inc = NULL, dist = "cor", WV = NULL, WV_marker = NULL, BPPARAM = SerialParam(), return_all = FALSE, BSPARAM = ExactParam(), plot_igraph = TRUE, verbose = FALSE)
sce_combine |
A |
batch |
A vector indicates the batch information for each cell in the batch-combined matrix. |
kmeansK |
A vector indicates the kmeans's K for each batch, length of kmeansK needs to be the same as the number of batch. |
exprs |
A string indicates the assay that are used for batch correction, default is logcounts |
hvg_exprs |
A string indicates the assay that are used for highly variable genes identification, default is counts |
marker |
A vector of markers, which will be used in calculation of mutual nearest cluster. If no markers input, highly variable genes will be used instead |
marker_list |
A list of markers for each batch, which will be used in calculation of mutual nearest cluster. |
replicate_prop |
A number indicating the ratio of cells that are included in pseudo-replicates, ranges from 0 to 1. Default to 1. |
cell_type |
A vector indicates the cell type information for each cell in the batch-combined matrix. If it is |
cell_type_match |
Whether find mutual nearest cluster using cell type information |
cell_type_inc |
A vector indicates the indices of the cells that will be used to supervise the pseudo-replicate procedure |
dist |
The distance metrics that are used in the calculation of the mutual nearest cluster, default is Pearson correlation. |
WV |
A vector indicates the wanted variation factor other than cell type info, such as cell stages. |
WV_marker |
A vector indicates the markers of the wanted variation. |
BPPARAM |
A |
return_all |
If |
BSPARAM |
A |
plot_igraph |
If |
verbose |
If |
If return_all
is FALSE
, return a replicate matrix.
If return_sce
is TRUE
, return the followings
repMat |
replicate matrix |
mnc |
mutual nearest cluster |
replicate vector |
replicate vector |
HVG |
highly variable genes used in scReplicate |
A cell-replicates mapping matrix. Each row correspond to a cell from the input expression matrix, and each column correspond to a cell-cluster/cell-type. An element of the mapping matrix is 1 if the scReplicate algorithm determines that this cell should belong to that cell cluster and 0 otherwise.
Yingxin Lin, Kevin Wang
## Loading example data set.seed(1) data('example_sce', package = 'scMerge') scRep_result = scReplicate( sce_combine = example_sce, batch = example_sce$batch, kmeansK = c(3,3))