read.export.datum: Read and align Cp data for telomeres and controls in an...

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

Description

read.export.datum reads a pair of exported files containing separated telomere and control data and aligns them for later use

Usage

read.export.datum(
  exp.control.filenames,
  source.search.path = NA,
  subject.list.from.input.path = NA,
  plate.content.report = NA,
  plate.list = NA
)

Arguments

exp.control.filenames	Length-2 vector of filenames: one for Telo, one for 36B4
source.search.path	Character vector with path to test case Data/Analysis *.xlsx files
subject.list.from.input.path	Logical: whether to pull subject data from Data/Analysis/*xlsx of an existing analysis run
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

Details

This function removes extraneous metadata and provides mild control checking. It does not postprocess the data in any meaningful way. This function should not be called directly by the end user.

Note that for workaround purposes while I'm figuring out how the end user is going to specify the evidently external location of the "Source Plate Contents" Data/Analysis pasted spreadsheet tab, I'm just going to pull the source plate contents from the existing spreadsheets. This will be removed at a future date, but allows development and testing to continue for the time being.

Value

An instance of S4 class ExportDatum containing aligned relevant information.

See Also

find.input.files() for generating the expected input for this function.

Examples

read.export.datum(c(
  "Data/Exports/PC29625_A_Telo.txt",
  "Data/Exports/PC29624_A_36B4.txt"
))

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