arabidopsis: Arabidopsis thaliana

In rfVarImpOOB: Unbiased Variable Importance for Random Forests

Arabidopsis thaliana

Description

RNA editing is the process whereby RNA is modified from the sequence of the corresponding DNA template [1]. For instance, cytidine-to-uridine conversion (abbreviated C-to-U conversion) is common in plant mitochondria. The mechanisms of this conversion remain largely unknown, although the role of neighboring nucleotides is emphasized. Cummings and Myers [1] suggest to use information from sequence regions flanking the sites of interest to predict editing in Arabidopsis thaliana, Brassicanapus and Oryza sativa based on random forests. The Arabidopsis thaliana data of [1] can be loaded from the journal Web site.

For each of the 876 observations, the data set gives

the response at the site of interest (binary: edited/not edited) and as potential predictor variables the 40 nucleotides at positions -20 to 20, relative to the edited site (4 categories), cp: the codon position (4 categories), fe: the estimated folding energy (continuous) and dfe: the difference in estimated folding energy between pre- edited and edited sequences (continuous).

Usage

arabidopsis

Format

Data frame with columns

edit

binary:the response at the site of interest

X.k

nucleotides at positions -k, relative to the edited site (4 categories)

Xk

nucleotides at positions k, relative to the edited site (4 categories)

cp

the codon position (4 categories),

fe

the estimated folding energy (continuous)

dfe

the difference in estimated folding energy between pre- edited and edited sequences (continuous)

Source

[1] Cummings, Michael P, and Daniel S Myers. Simple Statistical Models Predict C-to-U Edited Sites in Plant Mitochondrial RNA. BMC Bioinformatics, 2004, 7.

Examples

arabidopsis

rfVarImpOOB documentation built on July 1, 2022, 5:05 p.m.