prestoR

The presto report package (prestoR) is an R package for generating quality control plots from pRESTO log tables.

Example Report

Download & Installation

prestor is current not available from CRAN and must be installed from the bitbucket repo directly by first cloning the bitbucket repository:

http://bitbucket.org/javh/prototype-prestor

Then build using the following R commands from the package root:

install.packages(c("devtools", "roxygen2"))
library(devtools)
install_deps(dependencies=T)
document()
install()

Alternatively, you can install directly form the bitbucket repository, but this will not build the documentation:

library(devtools)
install_bitbucket("javh/prototype-prestor@default")

Documentation

For an index of available functions see:

help(package="prestor")

For some common tasks see the following help pages:

Function

Description

report_abseq3

Generate a report for an AbSeq V3 pRESTO pipeline script

loadConsoleLog

Parse console output from a pRESTO pipeline

loadLogTable

Parse tabled log output from pRESTO tools

plotConsoleLog

Plot console output from a pRESTO pipeline

plotAssemblePairs

Plot AssemblePairs log table

plotBuildConsensus

Plot BuildConsensus log table

plotFilterSeq

Plot FilterSeq log table

plotMaskPrimers

Plot MaskPrimer log table

plotParseHeaders

Plot ParseHeaders log table