Read, Write, Validate, and Analyze Real-Time PCR Data in the 'RDML' Format

Reads, writes, validates, converts, and manipulates quantitative polymerase chain reaction (qPCR) data through the Real-Time PCR Data Markup Language ('RDML') application programming interface (API), using 'S7' objects. Includes an extensible file-format registry, vendor and tabular-data importers, 'RDES' import and export, fluorescence-table helpers, semantic validation, and compatibility wrappers for the historical 'RDML' API.

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.