create.analysis: Create a PrimaryAnalysis from a loaded ExportDatum

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

Description

create.analysis takes an ExportDatum object containing telomeric and control data and applies the standard analysis currently being run by the excel template that generates files in Data/Analysis/*xlsx.

Usage

create.analysis(
  export.datum,
  plate.content.report = NA,
  plate.list = NA,
  infer.384.locations = FALSE,
  control.vials = c("NA07057")
)

Arguments

export.datum	An ExportDatum object with raw qPCR data for processing
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
control.vials	Character vector of internal control vial IDs

Details

This function attempts to emulate the results in the primary analysis spreadsheet. There's a fair amount of redundant information (log2 transform of some data, linear regression information that is deprecated) that is not being included for the moment.

Value

a PrimaryAnalysis object containing the processed results for the input

See Also

PrimaryAnalysis() for constructing empty PrimaryAnalysis objects; read.export.datum() for generating compatible input data structures.

Examples

filename.pair <- find.input.files("Examples for Bioinformatics")
export.datum <- read.export.datum(filename.pair)
processed.analysis <- create.analysis(export.datum)

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