scorpionTest: Example single-cell gene expression, motif, and ppi data

In SCORPION: Single Cell Oriented Reconstruction of PANDA Individual Optimized Networks

Example single-cell gene expression, motif, and ppi data

Description

This data is a list containing three objects. The motif data.frame describes a set of pairwise connections where a specific known sequence motif of a transcription factor was found upstream of the corresponding gene. The expression dgCMatrix is a set of 230 gene expression levels measured across 80 cells. Finally, the ppi data.frame describes a set of known pairwise protein-protein interactions.

Usage

data(scorpionTest)

Format

A list containing three datasets.

gex

A subsetted version of 10X Genomics' 3k PBMC dataset provided by the Seurat package.

tf

Subset of the transcription-factor and target gene list provided by the dorothea package for Homo sapiens.

ppi

The known protein-protein interactions and the combined score downloaded from the STRING database

Examples

# Loading example data
data(scorpionTest)

# The structure of the data
str(scorpionTest)

# List of 3
# $ gex:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
# .. ..@ i       : int [1:4456] 1 5 8 11 22 30 33 34 36 38 ...
# .. ..@ p       : int [1:81] 0 47 99 149 205 258 306 342 387 423 ...
# .. ..@ Dim     : int [1:2] 230 80
# .. ..@ Dimnames:List of 2
# .. .. ..$ : chr [1:230] "MS4A1" "CD79B" "CD79A" "HLA-DRA" ...
# .. .. ..$ : chr [1:80] "ATGCCAGAACGACT" "CATGGCCTGTGCAT" "GAACCTGATGAACC" "TGACTGGATTCTCA" ...
# .. ..@ x       : num [1:4456] 1 1 3 1 1 4 1 5 1 1 ...
# .. ..@ factors : list()
# $ tf :'data.frame':	4485 obs. of  3 variables:
#   ..$ tf    : chr [1:4485] "ADNP" "ADNP" "ADNP" "AEBP2" ...
# ..$ target: chr [1:4485] "PRF1" "TMEM40" "TNFRSF1B" "CFP" ...
# ..$ mor   : num [1:4485] 1 1 1 1 1 1 1 1 1 1 ...
# $ ppi:'data.frame':	12754 obs. of  3 variables:
#   ..$ X.node1       : chr [1:12754] "ADNP" "ADNP" "ADNP" "AEBP2" ...
# ..$ node2         : chr [1:12754] "ZBTB14" "NFIA" "CDC5L" "YY1" ...
# ..$ combined_score: num [1:12754] 0.769 0.64 0.581 0.597 0.54 0.753 0.659 0.548 0.59 0.654 ...

SCORPION documentation built on June 22, 2024, 9:35 a.m.