snap-class: An S4 class snap to represent single-nucleus accessibility...
In r3fang/SnapATAC: Single Nucleus Analysis Package for ATAC-Seq
snap-class R Documentation
An S4 class snap to represent single-nucleus accessibility object.
Description
Class snap defines a snap object.
Slots
desA character object describes the details of the experiment.
barcodeA character vector contains cell barcodes as rows.
fileA character vector contains the snap file that barcodes belong to.
sampleA character vector contains sample name.
metaDataA data.frame object contains meta data for barcodes.
featureA GRanges object contains genomic features (bins).
peakA GRanges object contains genomic features (peaks).
bmatA Matrix object contains cellxbin count matrix.
pmatA Matrix object contains cellxpeak count matrix.
gmatA matrix object contains cellxgene count matrix.
mmatA matrix object contains cellxmotif variability matrix.
jmatA jaccard object that contains jaccard index matrix.
smatA list object contains the linear dimentionality reduction result.
graphA kgraph object that contains the knn graph.
tsneA matrix object contains tsne coordinate.
umapA matrix object contains umap coordinate.
clusterA factor object contains cluster label.
r3fang/SnapATAC documentation built on March 29, 2022, 4:33 p.m.
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| snap-class | R Documentation |
An S4 class snap to represent single-nucleus accessibility object.
Description
Class snap defines a snap object.
Slots
desA character object describes the details of the experiment.
barcodeA character vector contains cell barcodes as rows.
fileA character vector contains the snap file that barcodes belong to.
sampleA character vector contains sample name.
metaDataA data.frame object contains meta data for barcodes.
featureA GRanges object contains genomic features (bins).
peakA GRanges object contains genomic features (peaks).
bmatA Matrix object contains cellxbin count matrix.
pmatA Matrix object contains cellxpeak count matrix.
gmatA matrix object contains cellxgene count matrix.
mmatA matrix object contains cellxmotif variability matrix.
jmatA jaccard object that contains jaccard index matrix.
smatA list object contains the linear dimentionality reduction result.
graphA kgraph object that contains the knn graph.
tsneA matrix object contains tsne coordinate.
umapA matrix object contains umap coordinate.
clusterA factor object contains cluster label.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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