getMarkers: Get the list of samples from the panglaoDB database with a...

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

Description

Get the list of samples from the panglaoDB database with a pattern of expression for a set of molecular markers.

Usage

getMarkers(include, exclude = NULL)

Arguments

include	A set of molecular markers to query the database. This set of genes needs to be expressed in the sample.
exclude	A set of molecular markers to query the database. This set of genes needs to be absent in the sample.

Value

The rows in the data frame are the samples matching the requested pattern. The returned data frame contain 7 columns as follows:

• SRA: The SRA identifier of the biological sample in the SRA database

• SRS: The SRS identifier of the biological sample in the SRA database

• Specie: The specie from which the biological samples originated from

• Tissue: The tissue from which the biological samples originated from

• Cluster: The cluster-id assigned by the panglaoDB database to the cells matching the requested pattern

• Cell-Type: The cell-type from which the counts originates from

• Markers: The recovered pattern for the marker genes requested

Examples

## Not run: 
Fibrocytes <- getMarkers(include = c('ACTA2', 'CD34', 'FAP'))
Fibrocytes
## End(Not run)

#       SRA        SRS       Specie Tissue Cluster   Cell-Type         Markers
# SRA681285 SRS3121028 Mus musculus Dermis       4 Fibroblasts +ACTA2+CD34+FAP

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