getSamples: Download the expression matrix and annotations from the...

In rPanglaoDB: Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Database

Description

Download the expression matrix and annotations from the panglaoDB database.

Usage

getSamples(
  sra = "All",
  srs = "All",
  tissue = "All",
  protocol = "All",
  specie = "All",
  celltype = "All",
  include = NA,
  exclude = NA,
  merge = TRUE
)

Arguments

sra	Filter based on the SRA identifier of the biological sample in the SRA database
srs	Filter based on the SRS identifier of the biological sample in the SRA database
tissue	Filter based on the tissue from which the biological samples originates from
protocol	Filter based on the single-cell library preparation protocol used to generate the data
specie	Filter based on the specie from which the biological samples originates from
celltype	Filter based on the cell-type from which the counts originates from
include	A set of molecular markers to filter the dataset. This set of genes needs to be expressed in each cell.
exclude	A set of molecular markers to filter the dataset. This set of genes needs to be absent in each cell.
merge	A boolean value TRUE or FALSE defining if the samples should be returned as a list or as a unique Seurat object

Value

A Seurat object, as described in ?SeuratObject::`Seurat-class`

Examples

# From PanglaoDB SRS3805255
# https://panglaodb.se/view_data.php?sra=SRA705190&srs=SRS4139632

## Not run: 
SRS4139632 <- getSamples(srs = 'SRS4139632')
SRS4139632
## End(Not run)

# An object of class Seurat
# 19859 features across 102 samples within 1 assay
# Active assay: RNA (19859 features, 0 variable features)

# Metadata from the PanglaoDB database can be accessed as follows:
# head(SRS4139632[[]])

rPanglaoDB documentation built on May 13, 2021, 1:07 a.m.