predicted_expression: Create a predicted expression matrix

In kieranrcampbell/embeddr: Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data

Description

Given a list of models return a matrix corresponding to the prediction from the models. Each column represents a gene and each row its expression at a given point in pseudotime.

Usage

predicted_expression(sce, models = NULL, n_cores = 2)

Arguments

sce	An object of class SCESet
models	An object representing models. If of type list then for each element the predicted expression is computed and a matrix returned. If of type model for which a predict function is available, then a single vector corresponding to predict(model) is returned. If NULL then the model is computed for all genes in sce and the resulting list returned.
n_cores	The number of cores to pass to mclapply.

Value

A dataframe of predicted expression where rows are cells (pseudotime) and columns are genes

Examples

library(scater)
data('sc_example_counts') ; sce <- newSCESet(countData = sc_example_counts)
sce <- embeddr(sce)
sce <- fit_pseudotime(sce)
pe <- predicted_expression(sce[1:4,]) # use first four genes

kieranrcampbell/embeddr documentation built on May 20, 2019, 9:24 a.m.