CYT-class: Class 'CYT'

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

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.

Slots

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.

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.