View source: R/FRmatch_cell2cluster.R
FRmatch_cell2cluster | R Documentation |
This is a user-end wrapper function that implements the steps of cell type matching between two single cell RNA-seq experiments
(namely, query
and reference
) using the cell-to-cluster FR-Match approach that matches each query cell to a reference cluster.
FRmatch_cell2cluster( sce.query, sce.ref, use.cosine = TRUE, feature.selection = "reference.markers", filter.size = 5, filter.fscore = NULL, filter.nomarker = FALSE, add.pseudo.marker = FALSE, pseudo.expr = 1, subsamp.size = 10, subsamp.iter = 2000, subsamp.seed = 1, numCores = NULL, prefix = c("query.", "ref."), verbose = 1, ... )
sce.query |
Data object of the SingleCellExperiment class for query experiment.
See details in |
sce.ref |
Data object of the SingleCellExperiment class for reference experiment.
See details in |
feature.selection |
Which set of features to use for the matching space? Default: |
filter.size, filter.fscore, filter.nomarker |
Filtering out small/poor-quality/no-marker clusters. Default: |
add.pseudo.marker, pseudo.expr |
Adding pseudo marker to stabilize no expression clusters in the marker gene feature space.
Default: |
subsamp.size, subsamp.iter, subsamp.seed |
Numeric variables for iterative subsampling size, number of iterations, and random seed for iterations. YMMV. |
numCores |
Number of cores for parallel computing. Default: |
prefix |
Prefix names for query and reference clusters. Default: |
verbose |
Numeric value indicating levels of details to be printed. Default: |
... |
Additional arguments passed to |
This implementation is FRmatch
with an iterative subsampling scheme, which is a bootstrap-like approach to randomly select a smaller
set of cells from a query cluster and quantify the confidence score of the selected cells belonging to certain reference cell type
using the p-value outputted from FRtest
(i.e. a larger p-value indicates higher probability of a match, and vice versa).
This function assigns the cluster-level p-value to each selected query cell, and updates the assigned p-value if the query cell is reselected from the iterative procedure and assigned a higher p-value. The output from this implementation includes a cell-by-cluster (a.k.a. query cell by reference cluster) matrix of p-values.
A list of:
settings |
Record of customized parameter settings specified in the function. |
pmat |
A cell-by-cluster (a.k.a. query cell by reference cluster) matrix of p-values retained from the iterative procedure. |
cell2cluster |
A data frame of cell-to-cluster matches summarized from the |
Columns in cell2cluster
are:
query.cell |
Query cell ID. |
query.cluster |
Cluster membership of query cells. |
match |
Matched reference cluster for the query cell. |
score |
Confidence score of |
Visualization of matching results using plot_FRmatch_cell2cluster
.
## Not run: data("sce.example") FRmatch_cell2cluster(sce.example, sce.example) ## End(Not run)
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