drosophila: Tissue type and transcription factor binding data during...

In baycn: Bayesian Inference for Causal Networks

Description

Zinzen et al. (2009) measured in vivo transcription factor binding for five key transcription factors using ChIP-chip assays at two hour intervals during drosophila mesoderm development. The five transcription factors are: Twist (Twi), Tinman (Tin), Myocyte enhancing factor 2 (Mef2), Bagpipe (Bap), and Biniou (Bin). Both Twi and Tin were assayed from 2-8 hours, Mef2 from 2-12 hours, Bap from 6-8 hours, and Bin from 6-12 hours. In addition, Zinzen et al. identified six tissue types based on tissue specific expression: mesoderm (Meso), somatic muscle (SM), visceral muscle (VM), cardiac muscle (CM), mesoderm and somatic muscle (Meso&SM), and somatic and visceral muscle (SM&VM). All data are binary and measured at 310 cis-regulatory modules.

Usage

data(drosophila)

Format

An object of class "list" containing tissue type and transcription factor binding data. The first element in the list is a matrix which contains the data in the original form. The second element in the list is a matrix that contains the binary data. For this matrix any value greater than zero to changed to a one. For both data sets the tissue type data appears in the first six columns of the data matrix and the remaining 15 columns contain the transcription factor binding data.

Source

https://www.nature.com/articles/nature08531#Sec22

References

Zinzen, R., Girardot, C., Gagneur, J. et al. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 462, 65–70 (2009) doi:10.1038/nature08531

Examples

# Load the data.
data(drosophila)

# Display the first 5 rows and 8 columns of the continuous data matrix.
drosophila$continuous[1:5, 1:8]

# Display the first 5 rows and 8 columns of the discrete data matrix.
drosophila$discrete[1:5, 1:8]

baycn documentation built on Aug. 1, 2020, 1:07 a.m.