| getMarkers {rPanglaoDB} | R Documentation |
Get the list of samples from the panglaoDB database with a pattern of expression for a set of molecular markers.
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