The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

RDML7

RDML7 is an R package for reading, manipulating, validating, converting, and writing quantitative PCR data. The current implementation uses S7 value objects, a camelCase functional API, and an extensible file-format registry.

The original RDML package is described in:

Stefan Rödiger, Michał Burdukiewicz, Andrej-Nikolai Spiess, Konstantin Blagodatskikh. Enabling reproducible real-time quantitative PCR research: the RDML package. Bioinformatics. https://doi.org/10.1093/bioinformatics/btx528

Installation

install.packages("remotes")
remotes::install_github("kablag/RDML7")

Basic workflow

library(RDML7)

x <- readRDML("experiment.rdml")

summary(x)
validateRDML(x)

metadata <- asTable(x)

amp <- getFData(
  x,
  dpType = "adp",
  longTable = TRUE
)

writeRDML(
  x,
  "experiment-copy.rdml"
)

RDML uses value semantics:

x <- setFData(
  x,
  fdata,
  description,
  fdataType = "adp"
)

Formats

listRDMLFormats()

Additional readers/writers can be registered with registerRDMLFormat() or loaded from module files with loadRDMLModule().

RDES

RDES import and export are supported:

x <- readRDML(
  "run_amplification.tsv",
  format = "rdes"
)

x <- readRDML(
  "run_amplification.tsv",
  format = "rdes",
  companionFile = "run_melting.tsv"
)

writeRDML(
  x,
  "run.tsv",
  format = "rdes",
  rdesType = "both"
)

See vignette("RDES", package = "RDML").

Legacy compatibility

Older names such as AsTable(), GetFData(), SetFData() and MergeRDMLs(), remain available for dependent packages. New code should use the camelCase API.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.