STGlocalMarkers.RdSTG local markers Run STG to find a set of genes that separate a given DA region from a local subset of cells.
STGlocalMarkers(X, da.regions, da.region.to.run, cell.label.info, cell.label.to.run, ...)
| X | matrix, normalized expression matrix of all cells in the dataset, genes are in rows, rownames must be gene names |
|---|---|
| da.regions | output from the function getDAregion() |
| da.region.to.run | numeric, which (single) DA region to find local markers for |
| cell.label.info | vector, cell labeling information to select the local subset of cells to compare with input DA region |
| cell.label.to.run | cell label(s) to select from cell.label.info that represent the local neiborhood for the input DA region |
| lambda | numeric, regularization parameter that weights the number of selected genes, a larger lambda leads to fewer genes, default 1.5 |
| n.runs | integer, number of runs to run the model, default 5 |
| python.use | character string, the Python to use, default "/usr/bin/python" |
| return.model | a logical value to indicate whether to return the actual model of STG |
| GPU | which GPU to use, default '', using CPU |
a list of results:
a list of data.frame with markers for each DA region
a numeric vector showing mean accuracy for each DA region
a list of model for each DA region, each model contains:
features used to train the model the selected features of the final run the linear prediction value for each cell from the model