FRmatch | 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 cluster-to-cluster FR-Match approach.
FRmatch( sce.query, sce.ref, use.cosine = TRUE, filter.size = 5, filter.fscore = NULL, filter.nomarker = FALSE, add.pseudo.marker = FALSE, pseudo.expr = 1, subsamp.size = 20, subsamp.iter = 1000, subsamp.seed = 1, numCores = NULL, prefix = c("query.", "ref."), verbose = 1, return.all = FALSE, ... )
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 |
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: |
return.all |
Boolean variable indicating if to return all results (such as runs, etc.). Default: |
... |
Additional arguments passed to |
A list of:
settings |
Record of customized parameter settings specified in the function. |
pmat |
A matrix of p-values. Rows are reference clusters, and columns are query clusters. |
statmat |
A matrix of FR statistics. Rows are reference clusters, and columns are query clusters. |
If return.all = TRUE
, more intermediate results are returned.
Visualization of matching results using plot_FRmatch
, plot_bi_FRmatch
.
## Not run: data("sce.example") FRmatch(sce.example, sce.example) ## End(Not run)
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