promotergene {kernlab} | R Documentation |
E. coli promoter gene sequences (DNA)
Description
Promoters have a region where a protein (RNA polymerase) must make contact and the helical DNA sequence must have a valid conformation so that the two pieces of the contact region spatially align. The data contains DNA sequences of promoters and non-promoters.
Usage
data(promotergene)
Format
A data frame with 106 observations and 58 variables.
The first variable Class
is a factor with levels +
for a promoter gene
and -
for a non-promoter gene.
The remaining 57 variables V2 to V58
are factors describing the sequence.
The DNA bases are coded as follows: a
adenine c
cytosine g
guanine t
thymine
Source
UCI Machine Learning data repository
https://archive.ics.uci.edu/ml/machine-learning-databases/molecular-biology/promoter-gene-sequences/
References
Towell, G., Shavlik, J. and Noordewier, M.
Refinement of Approximate Domain Theories by Knowledge-Based
Artificial Neural Networks.
In Proceedings of the Eighth National Conference on Artificial Intelligence (AAAI-90)
Examples
data(promotergene)
## Create classification model using Gaussian Processes
prom <- gausspr(Class~.,data=promotergene,kernel="rbfdot",
kpar=list(sigma=0.02),cross=4)
prom
## Create model using Support Vector Machines
promsv <- ksvm(Class~.,data=promotergene,kernel="laplacedot",
kpar="automatic",C=60,cross=4)
promsv