CreateTemporaObject: Create new Tempora object from a processed gene expression...

In BaderLab/Tempora: Pathway-based Trajectory Inference for Time-series Single Cell RNA-Seq Data

Description

Create new Tempora object from a processed gene expression matrix

Usage

CreateTemporaObject(
  exprMatrix,
  meta.data,
  timepoint_order,
  cluster_labels = NULL,
  cell_markers = NULL,
  threshold = 0.9
)

Arguments

exprMatrix	A normalized gene expression matrix containing cells from all timepoints of the time-series study. Batch effect correction is highly recommended before normalization.
meta.data	A dataframe of meta data for all cells in the expression matrix. Each column is a feature and each row stores single cell information. At minimum, this dataframe should contain two columns: a "Clusters" column storing the clustering identity and a "Timepoints" column storing the timepoint when each cell comes from
timepoint_order	An ordered vector of timepoint names from early to late
cluster_labels	(Optional) A vector of cluster annotations (cell types, cell states, cell cycles, etc.), ordered alphanumerically by cluster names. If NULL and cell_markers is given, automatic cluster annotation using GSVA will be performed. If both are NULL, cluster numbers will be used to label the trajectory plot.
cell_markers	(Optional) A list of possible cell types found in the dataset and their marker genes to be used for automatic cell type identification. If NULL and no cluster_labels is given, cluster numbers will be used to label the trajectory plot.
threshold	(Optional) Threshold of GSVA score quantile. Cell types with GSVA scores in this quantile or higher compared to all other cell type scores for the same cluster would be included in cluster label. Numeric between 0-1, default to 0.9.

Value

A Tempora object containing the expression matrix and metadata

Examples

## Not run: tempora_dara <- CreateTemporaObject(exprMatrix, meta.data)

BaderLab/Tempora documentation built on April 25, 2021, 2:10 p.m.