URDclass: URD class
In farrellja/URD: URD

Description Slots

All information associated with a reconstruction project is stored in an URD object. Most functions in the URD package take one as input, and many of them return an URD object that has been operated on. A new URD object is created using the createURD function.

count.data

(Sparse Matrix) The initially provided count data expression matrix

logupx.data

(Sparse Matrix) The normalized and log2-transformed expression matrix

meta

(data.frame) Continuous and categorical information about cells provided during object creation

group.ids

(data.frame) Categorial information about cells, such as cluster identities and assignment within the tree

var.genes

(Character vector) Genes that have been determined as highly variable

pca.load

(data.frame) Loading of genes (rows) into principal components (columns)

pca.score

(data.frame) Score for each principal component (columns) in each cell (rows)

pca.sdev

(Numeric vector) Standard deviation of each principal component

pca.sig

(Logical vector) Whether each PC has been determined to be significant

tsne.y

(data.frame) tSNE coordinates for each cell (rows)

dm

(DiffusionMap from destiny) Diffusion map calculated by destiny

diff.data

(data.frame) Visitation frequencies from

pseudotime

(data.frame) Determined pseudotime for each cell (row)

pseudotime.stability

(List) Contains pseudotime and visitation for subsets of floods/walks for assaying whether enough simulations have been performed

pseudotime: Determined pseudotime for each cell
walks.per.cell: Number of walks that visited each cell

tree

(List) Contains information from building the tree

tips: (Vector) The tips used as input into building the tree
cells.in.tip: (List of character vectors) The cells that belong to each tip
pseudotime: (Named vector) The pseudotime of each cell used in construction of the tree
segments: (Vector) All segments present in the final tree
segment.pseudotime.limits: (data.frame) Start and end pseudotimes for each tree segment
segment.joins: (data.frame) Parent and child relationships for all segments in the tree and pseudotime of their breakpoints
segment.joins.initial: (data.frame) Parent and child relationships during construction of the tree – this data is prior to collapsing any multifurcating branchpoints or removing any segments that are too short or assigned too few cells
pseudotime.breakpoint.details: (List) Contains information used during the determination of putative pseudotime breakpoints between each pair of segments. Only retained if save.all.breakpoint.info=T during buildTree
segment.divergence: (data.frame) Used during tree building, stores potential breakpoint pseudotime between each pair of segments remaining
cells.in.segment: (List of character vectors) Cells assigned to each segment of the tree by URD
cells.in.nodes: (List of character vectors) Cells assigned to each node of the tree by URD
node.mean.pseudotime: (Named numeric vector) Mean pseudotime of cells in each node
node.max.pseudotime: (Named numeric vector) Max pseudotime of cells in each node
edge.list: (data.frame) All node-node edges in the dendrogram
tree.igraph: (igraph) igraph representation of all segment-segment relationships
segment.layout: (data.frame)
tree.layout: (data.frame) Placement of node-node edges on the dendrogram representation
cell.layout: (data.frame) Placement of cells on the dendrogram representation
segment.names: (Named vector) Names for each terminal population for use in the dendrogram layout
segment.names.short: (Named vector) Short names for each terminal population to use in the force-directed layout
walks.force.edges: (data.frame) k-NN edge list based on visitation frequency used for force-directed layout
walks.force.layout: (data.frame) 3D coordinates for the force-directed layout
force.view.list: (List) Stored orientations for displaying the force-directed layout
force.view.default: (Character) The force-directed view that should be used if none is specified

nmf.g