README.md

In sterlo/kineticWavelets: Small Library for Analysis of PacBio Kinetic Data using wavelets

KineticWavelets

Prerequisites

Bioconductor packages

Biostrings and ShortRead packages from Bioconductor.

If you are unfamiliar with bioconductor merely run the following commands at your R prompt.

source("http://bioconductor.org/biocLite.R") biocLite(c('shortRead','Biostrings'))

h5r

Install hdf5 library for your OS, for me using OSX and the homebrew package manager the relevant command was brew install hdf5

Run the command.

wget http://cran.r-project.org/src/contrib/Archive/h5r/h5r_1.4.7.tar.gz

Then install from within R using install.packages setting repos to NULL and the type to 'source'.

install.packages('<path to h5r.tar.gz>', repos = NULL, type="source")

Any packages available from CRAN will be installed by default.

R-pbh5

Run the command

git clone https://github.com/PacificBiosciences/R-pbh5

then

R CMD INSTALL R-pbh5

Installation

In a R prompt type

install.packages('devtools')

library(devtools)

install_github('KineticWavelets',username='sterlo')

to use the package type.

library(KineticWavelets)

Tutorial

Download a reference fasta file and some CMPh5 data.

Create a new KineticWavelets object

`kin = KineticWavelets(h5="h5 path",reff="reference path")1

Example wave128 window run.

wav = wave128Window(kin,DNAPattern="GGCGGC") plotSmoothAverage(wav) plotDetailWave(wav)

Example baseCorrelation run.

bas = baseCorrelation(kin,DNAPattern="GGCGGC) plotPatternCorrelation(bas) plotBaseCorrelation(bas)

sterlo/kineticWavelets documentation built on May 30, 2019, 4:42 p.m.