process.experiment: Process a CGR-style telomere qPCR experiment

In NCI-CGR/cgrtelomeres: Automated Processing of Telomere qPCR Data

Description

process.experiment takes the output of a lab telomere qPCR experiment and generates the expected output content from prior processing methods.

Usage

process.experiment(
  input.path,
  output.path,
  project.id = NA,
  plate.content.report = NA,
  plate.list = NA,
  infer.384.locations = FALSE,
  subject.list.from.input.path = TRUE,
  control.vials = c("NA07057")
)

Arguments

input.path	Character vector of input directory path
output.path	Character vector of output directory path
project.id	Character vector of project ID (e.g. "GP0317-TL7") or NA
plate.content.report	Character vector of plate content report for project (e.g. "PlateContentReport_GP0317-TL1.xls") or NA
plate.list	Character vector of plate list for project (e.g. "PlateList_GP0317-TL1.xls") or NA
infer.384.locations	Logical: whether to assume fixed 96->384 well mapping
subject.list.from.input.path	Logical: whether to pull subject data from Data/Analysis/*xlsx of an existing analysis run
control.vials	character vector: internal control vial IDs

Details

This is the main entry point for the CGR telomere processing package. The input directory is sanity checked for its expected contents. The output directory will be created if it doesn't already exist. Any existing conflicting output files will be overwritten by this method, so please change output.path if you don't want this behavior.

During development, plate content report and list files were not necessarily available for test cases. As such, an override mode has been added that pulls pre-pasted copies of relevant content report data from the spreadsheets in Data/Analysis from an existing telomere run. During deployment, this will almost certainly not be the desired behavior, and this feature is scheduled to be removed. This flag will also be overridden when plate list and content report are both specified.

In all existing test datasets, a fixed mapping from 96 well to 384 well layouts has been found. For mild efficiency purposes, this mapping has been set as the default. If there is ever any doubt, or if the well mapping is changed at some point in the future, setting infer.384.locations to FALSE will trigger dynamic remapping using the data in plate.content.report and plate.list.

Value

TBD

Examples

process.experiment(
  "Examples for Bioinformatics",
  "C:/Users/palmercd/Documents/telomeres/output", "GP0317-TL7"
)

NCI-CGR/cgrtelomeres documentation built on Feb. 11, 2021, 12:12 p.m.