Package 'mop'

Coerce object to nanodrop

Description

Coerce object to nanodrop

Usage

as_nanodrop(x, ...)

## S3 method for class 'data.frame'
as_nanodrop(x, nucleotide = NULL, is_tidy = FALSE, date = NULL, ...)

Arguments

x	a data.frame
...	additional arguments passed to their respective functions
nucleotide	an optional character vector describing the measured nucleotide (DNA, RNA, dsDNA, dsRNA)
is_tidy	Logical. Is data already tidy?
date	Character coercible to a Date object via lubridate::as_date

Value

a nanodrop object

---

Convert a scrubbed pcr object back to a pcr object

Description

Convert a scrubbed pcr object back to a pcr object

Usage

as_pcr(x)

Arguments

x	A tibble - usually a previously scrubbed pcr object.

Value

A pcr object

---

Make a nanodrop object

Description

Make a nanodrop object

Usage

incucyte(data, platemap)

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

an incucyte object

---

Test if an object is a incucyte object

Description

Test if an object is a incucyte object

Usage

is_incucyte(incucyte)

Arguments

incucyte

Object to be tested

Value

logical

---

Test if an object is a nanodrop object

Description

Test if an object is a nanodrop object

Usage

is_nanodrop(nanodrop)

Arguments

nanodrop

Object to be tested

Value

logical

---

Make a nanodrop object

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 = "mop") |>
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)

---

Constructor for a Incucyte object

Description

Constructor for a Incucyte object

Usage

new_incucyte(
  data = data.frame(),
  raw_data = data.frame(),
  date = lubridate::Date(),
  nucleotide = character(),
  is_tidy = logical()
)

Arguments

data	data.frame, no restrictions on form.
raw_data	data.frame, no restrictions on form. Typically represents read-in data with no changes to it.
date	lubridate::Date object
is_tidy	logical. Is the data.frame provided tidy?

Value

a nanodrop object

---

Constructor for a nanodrop object

Description

As this is a low-level constructor, it will let you do some un-recommended things without error. You have been warned.

Usage

new_nanodrop(
  data = data.frame(),
  raw_data = data.frame(),
  date = lubridate::Date(),
  nucleotide = character(),
  is_tidy = logical()
)

Arguments

data	data.frame, no restrictions on form.
raw_data	data.frame, no restrictions on form. Typically represents read-in data with no changes to it.
date	lubridate::Date object
nucleotide	character. Should likely be DNA, RNA, dsDNA, or even dsRNA.
is_tidy	logical. Is the data.frame provided tidy?

Value

a nanodrop object

---

Constructor for a pcr object

Description

Constructor for a pcr object

Usage

new_pcr(
  data = data.frame(),
  raw_data = raw(),
  header = character(),
  footer = character(),
  date = lubridate::Date(),
  experiment_type = character(),
  wells = integer(),
  is_tidy = logical()
)

Arguments

data	data.frame or gp, no restrictions on form.
raw_data	raw, read in from the provided file with readr::read_file_raw()
header	data.frame, the upper portion of the data before the body of the data. Usually contains run information.
footer	data.frame, the lower portion of the data after the body of the data. Usually contains analysis information. May not exist.
date	lubridate::Date object
experiment_type	character. Could
wells	Number of wells in plate
is_tidy	logical. Is the data.frame provided tidy?

Value

A pcr object

---

Constructor for a spectramax object

Description

Constructor for a spectramax object

Usage

new_spectramax(
  data = data.frame(),
  raw_data = raw(),
  date = lubridate::Date(),
  wavelengths = numeric(),
  is_tidy = logical()
)

Arguments

data	a data.frame, no restrictions on form.
raw_data	raw, read in from the provided file with readr::read_file_raw()
date	lubridate::Date object
is_tidy	logical. Are the data provided tidy?
experiment_type	character, no restrictions on form

Value

a spectramax object

---

Add leading 0 to sample names

Description

Add leading 0 to sample names

Usage

pad_zero(sample_names)

Arguments

sample_names

a vector of sample names

Value

A sample name with up to one zero padded

Examples

c("blueberry", "Sample 1", "Sample 10", "sample 2", "john", "larry", "toxic waste", "Sample 02") |>
  pad_zero()

# pad_zero will not pad if it doesn't need to:
c("Sample 1", "Sample 2", "Sample 9") |> pad_zero()

# pad_zero is case sensitive, since these will be coming off a machine in a standardized format

c("sample 10", "sample 1") |> pad_zero()
c("Sample 10", "Sample 1") |> pad_zero()

---

Get or set an object's plate data

Description

Get or set an object's plate data

Usage

plate_data(x, ...)

## S3 method for class 'spectramax'
plate_data(x, ...)

plate_data(x) <- value

## S3 replacement method for class 'spectramax'
plate_data(x) <- value

Arguments

x	Object to extract plate data from
...	Arguments to be passed to their respective methods
value	Value to set the plate to.

Value

A gp object

---

Read an Incucyte File

Description

Read an Incucyte File

Usage

read_incucyte(data, platemap)

Arguments

data	Plotting data output from the Incucyte analysis
platemap	.PlateMap file output from the platemap maker

---

Read in a NanoDrop file

Description

Read in a NanoDrop file

Usage

read_nanodrop(path, nucleotide = NULL, date = NULL, date_order = NULL)

Arguments

path	path to a NanoDrop .csv
nucleotide	An optional character vector describing the analyte detected. If NULL (the default), it will automatically try to extract one from the file path. Valid values include RNA, DNA, dsDNA, and dsRNA (or NULL).
date	An optional character vector coercible to a date object. If NULL (the default), it will automatically try to extract one from the file path. See details for detection methods.
date_order	An optional character vector to enforce an order of date to be read (if date is unspecified). Can be "ymd", "mdy", or "dmy"

Details

This function expects a file that has not been tampered with from the nanodrop machine itself, aside for the name.

This function calls read.delim and guesses its encoding (usually ⁠UTF-16LE⁠, unless it's been re-exported). It's less mysterious than reading in an apparent .csv with read.delim, and it keeps you from having to remember the encoding (which R often fails to auto-detect). When possible, it attempts to extract the nucleotide type from the path provided.

if date is NULL, the function will attempt to extract a date from the file name (not the whole file path). It will look for ymd, mdy, and dmy (in order). If it detects the first format, it will not look for the second, etc. Note how a reading taken from April 4th but written as 4_3_2021 will be misinterpreted. This error can be remedied by specifying the argument date_order

Value

a nanodrop object

Examples

system.file("extdata", "nanodrop.csv", package = "mop") |>
  read_nanodrop()

---

Read in a QuantStudio pcr file

Description

Read in a QuantStudio pcr file

Usage

read_pcr(path)

Arguments

path	path to a QuantStudio .xls

Value

a pcr object

---

Read and tidy a SPECTRAmax file

Description

Read and tidy a SPECTRAmax file

Usage

read_spectramax(path, date = Sys.Date(), wavelengths = NULL)

Arguments

path	Path to the SPECTRAmax .txt file
date	Date of experiment. If not supplied, uses current date.
wavelengths	What wavelengths were read in this experiment?

Details

SPECTRAmax files cannot be read in easily without tidying them simultaneously, due to their non-rectangular structure. Therefore, tidying is required to be read in and is not an option supplied.

Value

A list, with the following form:

data

a tibble that contains two columns - the type, and the (tidy) data itself in a list-column.

raw_data

a raw representation of the file, before tidying

date

character. The date of the experiment

experiment_type

character. The type of experiment (currently only pq (Protein Quantification) and mtt supported)

tidy

logical. Should always return TRUE if read in using read_spectramax

---

Convert a lab object to a tidy tibble

Description

Objects are a convenient way to represent lab data as it allows downstream functions to interact with them in specific ways depending on their type. Sometimes, however, it is more convenient to work with a flat tibble. scrub converts a lab object into a tibble

Usage

scrub(x, ...)

Arguments

x	object to be converted into a tibble
...	additional arguments to pass on to the respective object's class method

Value

a tibble

---

Convert a nanodrop object into a tibble

Description

Convert a nanodrop object into a tibble

Usage

## S3 method for class 'nanodrop'
scrub(x, raw = FALSE, ...)

Arguments

x	a nanodrop object
raw	Should the data be pulled from x$raw_data?
...	Unused

Value

a tibble

---

Convert a pcr object into a tibble

Description

Convert a pcr object into a tibble

Usage

## S3 method for class 'pcr'
scrub(x, include_header = FALSE, ...)

Arguments

x	a pcr object
include_header	Should the data from x$header be included?
...	Unused

Value

a tibble

---

Convert a spectramax object into a tibble

Description

Convert a spectramax object into a tibble

Usage

## S3 method for class 'spectramax'
scrub(x, n = 1, ...)

Arguments

x	a spectramax object
n	List item number to select data from
...	Unused

Value

a tibble

---

Tidy an incucyte object

Description

Tidy an incucyte object

Usage

## S3 method for class 'incucyte_data'
tidy_lab(x, force_tidy = FALSE, ...)

Arguments

x	An incucyte object to tidy
force_tidy	logical. Should the tidying take place, even if the is_tidy attribute is TRUE?
...	Unused

Details

This function:

Value

an incucyte object

---

Tidy a nanodrop object

Description

Tidy a nanodrop object

Usage

## S3 method for class 'nanodrop'
tidy_lab(x, force_tidy = FALSE, ...)

Arguments

x	A nanodrop object to tidy
force_tidy	logical. Should the tidying take place, even if the is_tidy attribute is TRUE?
...	Unused

Details

This function:

• renames columns to sensible substitutes

• converts date-times to ISO 8601-esque date-time format (YYYY-MM-DD HH:MM:SS vs YYYY-MM-DDTHH:MM:SSZ)

It's recommended that you do any manipulations to these data after you tidy, rather than before, as tidy_nanodrop expects the output to be fairly similar to the output from read_nanodrop.

A tidy nanodrop object will (usually) contain the following columns:

• date The date-time of sample reading, as YYYY-MM-DD HH:MM:SS

• sample_name The name of the sample provided by the NanoDrop itself

• conc The concentration of nucleic acid in ng/uL

• a260_280 The absorbance at 260nm / absorbance at 280nm. Typically a marker of protein contamination. Pure nucleic acid is typically around 2.

• a260_230 The absorbance at 260nm / absorbance at 230nm. Typically a marker of guanadine salt contamination. Pure nucleic acid is typically around 2.

• a260 The absorbance at 260nm, the wavelength nucleic acids absorb most strongly.

• a280 The absorbance at 280nm, the wavelength proteins absorb most strongly.

The remaining columns are typically unused.

Value

a nanodrop object

---

Tidy a PCR object

Description

Tidy a PCR object

Usage

## S3 method for class 'pcr'
tidy_lab(x, usr_standards = NULL, pad_zero = FALSE, ...)

Arguments

x	a pcr object
usr_standards	Custom supplied standards
pad_zero	Should, say, Sample 1 become Sample 01?
...	Unused

Value

a pcr object

---

Tidy a lab object

Description

Tidy a lab object

Usage

## S3 method for class 'spectramax'
tidy_lab(x, ...)

tidy_lab(x, ...)

Arguments

x	An object to tidy
...	Arguments passed to their respective methods

---