melt_genes: Create long table combining gene expression and cell metadata

In MyersGroup/testisAtlas: testisAtlas: R functions and analysis scripts used in the analysis of testis single cell RNAseq

Description

Create long table combining gene expression and cell metadata

Usage

melt_genes(genes, cell_metadata = cell_data, expression_matrix = data,
  predict = FALSE, factorisation = SDAresults)

Arguments

genes	character vector; vector of gene symbols, of which expression values will be plotted over pseudotime
cell_metadata	data.table with columns cell, Tsne1_QC1, Tsne2_QC2, and components V1, V2 etc.
expression_matrix	matrix; rows=cells, columns=genes, unimputed but normalised (scaled) expression values
predict	logical; if TRUE (default FALSE) imputed/predicted gene expression is used
factorisation	SDA factorisation object, output of SDAtools::load_results()

Value

data.table with columns 'cell', 'PsuedoTime', 'Tsne1_QC1', 'Tsne2_QC1', 'Gene', and 'Expression'

MyersGroup/testisAtlas documentation built on Nov. 29, 2020, 9:21 p.m.