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

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Documentation for package ‘scmap’ version 1.30.0

• 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.