# A tool for unsupervised projection of single cell RNA-seq data

## Documentation for package ‘scmap’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ann | Cell type annotations for data extracted from a publication by Yan et al.
EuclSqNorm | The Euclidean Squared Norm of each column of a matrix is computed and the whole result is returned as a vector. Used as part of the approx. calculations of the cosine similarity between the query and the reference.
getSankey | Plot Sankey diagram comparing two clusterings
indexCell | Create an index for a dataset to enable fast approximate nearest neighbour search
indexCell-method | Create an index for a dataset to enable fast approximate nearest neighbour search
indexCell.SingleCellExperiment | Create an index for a dataset to enable fast approximate nearest neighbour search
indexCluster | Create a precomputed Reference
indexCluster-method | Create a precomputed Reference
indexCluster.SingleCellExperiment | Create a precomputed Reference
NN | Main nearest neighbour calculation function. Used on the first reference dataset. Returns a list of three objects: 1) the cell indices of the w nearest neighbours 2) the corresponding approx. cosine similarities
normalise | Normalises each column of a matrix
scmapCell | For each cell in a query dataset, we search for the nearest neighbours by cosine distance within a collection of reference datasets.
scmapCell-method | For each cell in a query dataset, we search for the nearest neighbours by cosine distance within a collection of reference datasets.
scmapCell.SingleCellExperiment | For each cell in a query dataset, we search for the nearest neighbours by cosine distance within a collection of reference datasets.
scmapCell2Cluster | Approximate k-NN cell-type classification using scfinemap
scmapCell2Cluster-method | Approximate k-NN cell-type classification using scfinemap
scmapCell2Cluster.SingleCellExperiment | Approximate k-NN cell-type classification using scfinemap
scmapCluster | scmap main function
scmapCluster-method | scmap main function
scmapCluster.SingleCellExperiment | scmap main function
selectFeatures | Find the most informative features (genes/transcripts) for projection
selectFeatures-method | Find the most informative features (genes/transcripts) for projection
selectFeatures.SingleCellExperiment | Find the most informative features (genes/transcripts) for projection
setFeatures | Set the most important features (genes/transcripts) for projection
setFeatures-method | Set the most important features (genes/transcripts) for projection
setFeatures.SingleCellExperiment | Set the most important features (genes/transcripts) for projection
subdistsmult | Computes the dot product between the subcentroids from the indexed reference and the subvectors of an element of the query dataset. Returns an M by k matrix. Used as an intermediate step (in NNfirst and NNmult) for calculating an approximation of the cosine similarity between the query and the reference.
yan | Single cell RNA-Seq data extracted from a publication by Yan et al.