prestoR¶
The presto report package (prestoR) is an R package for generating quality control plots from pRESTO log tables.
Download & Installation¶
prestor is current not available from CRAN and must be installed from the bitbucket repo directly by first cloning the bitbucket repository:
https://bitbucket.org/kleinstein/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("kleinstein/prestor@master")
Documentation¶
For an index of available functions see:
help(package="prestor")
For some common tasks, see the following help pages:
Function |
Description |
---|---|
buildReport |
Generate a presto pipeline report |
loadConsoleLog |
Parse console output from a pRESTO pipeline |
loadLogTable |
Parse tabled log output from pRESTO tools |
pdfReport |
R Markdown to PDF format for pRESTO reports |
plotAlignSets |
Plot AlignSets log table |
plotAssemblePairs |
Plot AssemblePairs log table |
plotBuildConsensus |
Plot BuildConsensus log table |
plotConsoleLog |
Plot console output from a pRESTO pipeline |
plotFilterSeq |
Plot FilterSeq log table |
plotMaskPrimers |
Plot MaskPrimer log table |
plotParseHeaders |
Plot ParseHeaders log table |
report_abseq3 |
Generate a report for an AbSeq V3 pRESTO pipeline script |