sachs {SEMgraph}

Sachs multiparameter flow cytometry data and consensus model

Description

Flow cytometry data and causal model from Sachs et al. (2005).

Usage

sachs

Format

"sachs" is a list of 5 objects:

1. "rawdata", a list of 14 data.frames containing raw flow cytometry data (Sachs et al., 2005);

2. "graph", consensus signaling network;

3. "model", consensus model (lavaan syntax);

4. "pkc", data.frame of 1766 samples and 11 variables, containing cd3cd28 (baseline) and pma (PKC activation) data;

5. "group", a binary group vector, where 0 is for cd3cd28 samples (n = 853) and 1 is for pma samples (n = 913).

6. "details", a data.frame containing dataset information.

Source

doi:10.1126/science.1105809

References

Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP (2019). Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data. Science, 308(5721): 523-529.

Examples

# Dataset content
names(sachs$rawdata)
dim(sachs$pkc)
table(sachs$group)
cat(sachs$model)
gplot(sachs$graph)