classSNitch: Classifies RNA Structure Change in Chemical Mapping Data

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Variations in RNA sequence lead to differences in RNA structure called riboSNitches, if important structural elements are disrupted. Recent ultra-high throughput techniques, such as SHAPE-MaP and PARS, enable the collection of structural information on RNAs at a genome-wide scale. With the ability to gather large amounts of structural information, it is important to accurately identify those structural changes that can potentially result in a phenotypic outcome. We have developed an automated approach to identify and classify structure change in chemical mapping data. This method utilizes random forest classification on a set of seven characterizing features. The default mutate and map SHAPE data sets (or another user specified data set) can be used to build a classifier. The classifier is then used to identify structure change in other SHAPE traces. Enabling scientists to identify structure change may help guide experiments that examine RNA structure and its role in biological processes.

Author
Chanin Tolson [aut, cre]
Date of publication
2016-10-09 15:59:47
Maintainer
Laederach Lab <laederachlab@gmail.com>
License
GPL (>= 2)
Version
1.0.0
URLs

View on R-Forge

Man pages

classify_default
classify_default
classifyRNA
classifyRNA
classSNitch
Package for the autonomous classification of RNA structure...
getChangeRange
getChangeRange
getChangeVar
getChangeVar
getContiguous
getContiguous
getESDC
getESDC
getFeatures
getFeatures
getL2norm
getL2norm
getMagCC
getMagCC
getPatternCC
getPatternCC
getTimeWarping
getTimeWarping
mutmap
Consensus classification and features for example RNA SHAPE...
normalize
normalize
predict.classifyRNA
predict.classifyRNA
reduceNoise
reduceNoise
shape_ex
16S rRNA four-way junction wild-type and mutant SHAPE data...

Files in this package

classSNitch/DESCRIPTION
classSNitch/NAMESPACE
classSNitch/R
classSNitch/R/classSNitch.R
classSNitch/R/classifyRNA.R
classSNitch/R/classify_default.R
classSNitch/R/getChangeRange.R
classSNitch/R/getChangeVar.R
classSNitch/R/getContiguous.R
classSNitch/R/getESDC.R
classSNitch/R/getFeatures.R
classSNitch/R/getL2norm.R
classSNitch/R/getMagCC.R
classSNitch/R/getPatternCC.R
classSNitch/R/getTimeWarping.R
classSNitch/R/mutmap-data.R
classSNitch/R/normalize.R
classSNitch/R/predict.classifyRNA.R
classSNitch/R/reduceNoise.R
classSNitch/R/shape_ex-data.R
classSNitch/R/sysdata.rda
classSNitch/data
classSNitch/data/mutmap.rda
classSNitch/data/shape_ex.rda
classSNitch/inst
classSNitch/inst/doc
classSNitch/inst/doc/classSNitch.pdf
classSNitch/man
classSNitch/man/classSNitch.Rd
classSNitch/man/classifyRNA.Rd
classSNitch/man/classify_default.Rd
classSNitch/man/getChangeRange.Rd
classSNitch/man/getChangeVar.Rd
classSNitch/man/getContiguous.Rd
classSNitch/man/getESDC.Rd
classSNitch/man/getFeatures.Rd
classSNitch/man/getL2norm.Rd
classSNitch/man/getMagCC.Rd
classSNitch/man/getPatternCC.Rd
classSNitch/man/getTimeWarping.Rd
classSNitch/man/mutmap.Rd
classSNitch/man/normalize.Rd
classSNitch/man/predict.classifyRNA.Rd
classSNitch/man/reduceNoise.Rd
classSNitch/man/shape_ex.Rd