Description Usage Arguments Details Value
Users are advised to use the top-level functions RNAMagnetAnchors
and RNAMagnetSignaling
which appropriately set default parameters and return user-friendly return values.
This is a low level function for development purposes.
1 2 3 4 | RNAMagnetBase(seurat, anchors = NULL, neighborhood.distance = NULL,
neighborhood.gradient = NULL, .k = 10, .x0 = 0.5, .minExpression,
.version = "latest", .cellularCompartment,
.manualAnnotation = "Correct", .symmetric = F)
|
seurat |
An object of class |
anchors |
A character vector of anchor populations. Entries must be levels of |
neighborhood.distance |
See |
neighborhood.gradient |
See |
.k |
Fuzzification parameter, see detail. Recommended to leave at the default value. |
.x0 |
Fuzzification parameter, see detail. Recommended to leave at the default value. |
.minExpression |
Minimal expression level of genes to be included, specified as the number of cells in the dataset that express the gene. |
.version |
The version of the underlying ligand-receptor database. Recommended to leave at the default value. See |
.cellularCompartment |
Types of ligands to be included. For physical interactions, defaults to |
.manualAnnotation |
Annotation status of ligands to be included. Default to |
.symmetric |
Assume that if A is a receptor for B, B is also a receptor for A |
The algorithm takes the following steps:
Ligand-receptor pairs are selected based on the parameters .version
, .cellularCompartment
and .manualAnnotation
. Choice of .cellularCompartment
is crucial for determining the algorithm's behavior, e.g. if set to c("Secreted","Both")
, paracrine signaling interactions involving soluble ligands are investigated.
Dropout values in the expression levels of ligands and receptors are imputed using magic
Mean expression level of ligands and receptors is computed for all anchor populations
For each cell or anchor population, the expression of each ligand and receptor is encoded as a fuzzy logic variable
Fuzzy logic AND is used to compute probabilities for a given interaction to be active between a single cell and an anchor population
An interaction score is computed as the sum of interaction probabilities across all possible ligand-receptor pairs
Specificty scores are computed by comparing interaction scores to average interaction scores in a local neighborhood.
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Returns an object of class rnamagnet
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