getSampleComposition {rPanglaoDB}

Get the cell-type content for each sample from the panglaoDB database.

Description

Get the cell-type content for each sample from the panglaoDB database.

Usage

getSampleComposition(
  sra = "All",
  srs = "All",
  tissue = "All",
  protocol = "All",
  specie = "All",
  verbose = 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

verbose

A boolean value TRUE or FALSE to activate the verbose mode

Value

This function returns the cell-type composition of the samples included in the PanglaoDB database in a data frame with 8 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

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

• Protocol: The single-cell library preparation protocol used to generate the data

• Species: The species from which the biological samples originated from

• Cluster: The cluster-id assigned by the panglaoDB database to the cells in the sample

• Cells: The number of cells included in the cluster

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

Examples

# From PanglaoDB
# https://panglaodb.se/list_clusters_and_cell_types.html?sra=SRA689041&srs=SRS3166675

SRS3166675 <- getSampleComposition(srs = 'SRS3166675')
head(SRS3166675)

#       SRA        SRS Tissue     Protocol      Species Cluster Cells           Cell Type
# SRA689041 SRS3166675  Colon 10x chromium Mus musculus       0   735         Fibroblasts
# SRA689041 SRS3166675  Colon 10x chromium Mus musculus       1   526 Smooth muscle cells
# SRA689041 SRS3166675  Colon 10x chromium Mus musculus       2   465             Unknown
# SRA689041 SRS3166675  Colon 10x chromium Mus musculus       3   157             Unknown
# SRA689041 SRS3166675  Colon 10x chromium Mus musculus       4   140        Goblet cells
# SRA689041 SRS3166675  Colon 10x chromium Mus musculus       5   100         Fibroblasts