All information stored in CYT object.
You can use creatCYT
to create an CYT
object. In this package, most of the functions will use
CYT object as input, and return a modified CYT obejct as well.
raw.data
matrix. Raw signal data captured in flow or mass cytometry.
log.data
matrix. Log-transfromed dataset of raw.data.
meta.data
data.frame. Meta data information, and colnames of "stage" and "cell" are required.
markers
vector. Markers used in the calculation of PCA, tSNE, diffusion map and UMAP.
markers.idx
vector. Index of markers used in the calculation of PCA, tSNE, destiny and umap.
cell.name
vector. Cell names after performing downsampling.
knn
numeric. Numbers of nearest neighbors
knn.index,knn.distance
matrix. Each row of the
knn.index
matrix corresponds to a point
in log.data
and contains the row indices in
log.data
that are its nearest neighbors.
And each row of the knn.distance
contains
the distance of its nearest neighbors.
som
list. Store som network information calculated
using FlowSOM
.
cluster
data.frame. Cluster information
pca.sdev,pca.value,pca.scores
PCA information of CYT
object which are generated from fast.prcomp
.
tsne.value
matrix. tSNE coordinates information.
See Rtsne
.
dm
DiffusionMap object. Diffusion map calculated by package
destiny
umap.value
matrix umap coordinates information
calculated using umap
.
root.cells
vector, Names of root cells, which can
be modified by defRootCells
.
A root cell is manually set to be the origin of all cells.
Pseudotime in root cells are the lowest.
leaf.cells
vector. Names of leaf cells, which can be
modified by defLeafCells
.
A leaf cell is manually set to be the terminal state of
all cells. Pseuodtime in leaf cells is the largest.
network
list. Network stored in the calculation of trajectory and pseudotime.
walk
list. Random forward and backward walk between
root.cells
and leaf.cells
.
diff.traj
list. Differentiation trajectory of all cells.
plot.meta
data.frame. Plot meta information for
plot2D
or plot3D
.
tree.meta
data.frame. Tree meta information of CYT object.
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