analyzed_set: Retinal Ganglion Cells (100 THY-1 positive, 100 THY-1...

In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

Description

An EMSet containing the data from "raw" loaded into an EMSet. This data has been filtered and analysed as follows:

Usage

analyzed_set

Format

An object of class EMSet with 17421 rows and 102 columns.

Source

https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6108/

Examples

## Not run: 
# Load package
library(ascend)
# Read dataset from disk
em_set <- loadCellRanger(
"~/Downloads/filtered_gene_bc_matrices_mex/GRCh38p7/")

# Subset 100 cells from each batch
col_info <- colInfo(em_set)
subset_barcodes1 <- sample(col_info$cell_barcode[which(col_info$batch == 1)], 
100, replace = FALSE)
subset_barcodes2 <- sample(col_info$cell_barcode[which(col_info$batch == 2)], 
100, replace = FALSE)
barcode_list <- c(subset_barcodes1, subset_barcodes2)
raw_set <- em_set[, barcode_list]
# Get raw elements to use in vignettes
raw_counts <- counts(raw_set)
raw_col_info <- colInfo(raw_set)
raw_row_info <- rowInfo(raw_set)
# Quick ascend workflow for cells
working_set <- normaliseBatches(raw_set)
batch_norm_qc <- plotBatchNormQC(raw_object = raw_set, 
norm_object = working_set)
# Batch normalisation fine.
qc_plots <- plotGeneralQC(working_set)
# Perform QC
working_set <- filterByOutliers(working_set, cell.threshold = 3, 
gene.threshold = 3, control.threshold = 3)
working_set <- filterLowAbundanceGenes(working_set, pct.threshold = 0.1)
# Check cell numbers
col_info <- colInfo(working_set)
working_set <- normaliseByRLE(working_set)
working_set <- excludeControl(working_set, control = c("Mt", "Rb"))
working_set <- runPCA(working_set, scaling = TRUE, ngenes = 100)
working_set <- runTSNE(working_set, PCA = TRUE, dims = 2, seed = 1)
working_set <- runUMAP(working_set, method = "naive")
working_set <- runCORE(working_set, conservative = FALSE, nres = 40, 
dims = 20, remove.outliers = TRUE)

## End(Not run)

IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.