In NathanSkene/CTD.human.midbrain.embryonic:

BiocStyle::markdown()
knitr::opts_chunk$set(tidy         = FALSE,
                      warning      = FALSE,
                      message      = FALSE)

Installation

install.packages("devtools")
library(devtools)
install_github("nathanskene/CTD.human.midbrain.embryonic")

Human Midbrain Embryonic Dataset

This package provides easy access to the human midbrain embryonic dataset, which is associated with the following paper:

La Manno G, Gyllborg D, Codeluppi S, Nishimura K et al. Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. Cell 2016 Oct 6;167(2):566-580.e19. PMID: 27716510

The raw data is available along with annotations:

library(CTD.human.midbrain.embryonic)
data(raw_sc_expression_data)
raw_sc_expression_data$exp[1:5,1:5]
raw_sc_expression_data$annot[["level2class"]][1:10]
raw_sc_expression_data$annot[["level1class"]][1:10]

Should you wish to regenerate the data from scratch then the code for doing so is available in process_raw_sc_data(). I suggest forking this project, modifying the code for this function in there.

The processed cell type data (ctd) for use in MAGMA_Celltyping and EWCE is also available using:

library(CTD.human.midbrain.embryonic)
data(ctd)

Preparing cell type data file

library(EWCE)
raw_sc_expression_data$exp_CORRECTED = fix.bad.hgnc.symbols(raw_sc_expression_data$exp)
raw_sc_expression_data$exp_CORRECTED_DROPPED = drop.uninformative.genes(exp=raw_sc_expression_data$exp_CORRECTED, level2annot = raw_sc_expression_data$annot$level2class)
fNames = generate.celltype.data(exp=raw_sc_expression_data$exp_CORRECTED_DROPPED,raw_sc_expression_data$annot,"HumanEmbyronicMidbrain")

We can check the results are as expected:

load(fNames[1])
print(ctd[[1]]$specificity[1:5,1:5])
print(sort(ctd[[1]]$specificity[,"Embryonic Dopaminergic Neuron"],decreasing = TRUE)[1:20])

NathanSkene/CTD.human.midbrain.embryonic documentation built on May 24, 2019, 4:08 p.m.