nanodrop: Make a nanodrop object

In KaiAragaki/ragaki: Reduce Annoyances

Description

Make a nanodrop object

Usage

nanodrop(
  data,
  date = NULL,
  nucleotide = c("RNA", "DNA", "dsDNA", "dsRNA"),
  is_tidy = FALSE
)

Arguments

data	a data.frame - or something coercible to one - containing nanodrop data. See details for requirements.
date	an optional character vector or something coercible to a Date object with lubridate::as_date
nucleotide	a character vector to specifying the analyte in the nanodrop experiment. Must match one of the following: RNA, DNA, dsDNA, or dsRNA.
is_tidy	logical. Is the supplied data tidy?

Details

Making a nanodrop object 'by hand' (that is, not using read_nanodrop) is not recommended, since it is challenging to ensure a given data.frame is truly a valid nanodrop file. To increase reliability, flexibility is reduced. As such, the supplied data.frame must at least have the following columns if is_tidy = TRUE:

• date

• sample_name

• conc

• a260_280

• a230_280

If is_tidy = FALSE, at least the following columns must be provided:

• Date

• Sample.Name

• Nucleic.Acid.ng.uL.

• A260.A280

• A260.A230

Note: technically, the given column names will be stripped of all non-alphanumerics and forced tolower, then compared against the following:

• date

• samplename

• nucleicacidngul

• a260a280

• a260a230

In both cases, other columns allowed are those that appear in Example A and Example B below.

If there are additional columns provided, they will be silently dropped.

Value

a nanodrop object

Examples

# Example A: colnames allowed when is_tidy = FALSE
a <- system.file("extdata", "nanodrop.csv", package = "ragaki") |>
read_nanodrop()

colnames(a$data)

# Technically, these are the names that are checked for after the given names
# have alphanumerics removed and are converted to lowercase:

colnames(a$data) |> stringr::str_remove_all("[^[:alnum:]]") |> tolower()


# Example B: colnames allowed when is_tidy = TRUE
b <- a |> tidy_lab()

colnames(b$data)

KaiAragaki/ragaki documentation built on Dec. 25, 2021, 2:24 a.m.