extract.well.mappings: Map 96 to 384 wells using Plate List and Content Report data

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

Description

extract.well.mappings takes plate list and content data and extracts the actual 96->384 well mapping used in the analysis, as opposed to the default one observed in the initial test case.

Usage

extract.well.mappings(plate.list.data, plate.content.data, analysis.code)

Arguments

plate.list.data	Data frame of plate list data
plate.content.data	Data frame of plate content report data
analysis.code	Character vector: case-sensitive letter A-H for run code

Details

The output is sorted lexicographically by 96 well label. Replicate assignments (1 vs 2 vs 3) are similarly resolved by lexicographical sort of the 384 well labels. This should compel the output to exactly match the previous protocol's Data/Analysis/*xlsx format if used without further shuffling.

Value

List with entries Rep1.Well, Rep2.Well, Rep3.Well, corresponding to columns in the Data/Analysis/*xlsx files. Each will be a factor.

See Also

create.analysis() for calling function; openxlsx::read.xlsx() for an example of how to generate the plate list or content data frames.

Examples

content.filename <- "PlateContentReport_GP0317-TL1.xls"
list.filename <- "PlateList_GP0317-TL1.xls"
content.data <- openxlsx:read.xlsx(content.filename,
  sheet = 1,
  rowNames = FALSE, colNames = TRUE
)
list.data <- openxlsx::read.xlsx(list.filename,
  sheet = 1,
  rowNames = FALSE, colNames = TRUE
)
analysis.code <- "H"
well.mappings <- extract.well.mappings(
  list.data, content.data,
  analysis.code
)

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