R: Read a data set from a data-sheet and turn it into a...

set_read {bioset}

R Documentation

Read a data set from a data-sheet and turn it into a multi-column tibble.

Description

Read a matrix of values from a csv sheet and sort them into a tibble. You can name the values and encode several additional properties into the name, which be split into several columns. Please refer to the vignette (browseVignettes("roxygen2")) and examples below for in-depth explanation and the whys and hows.

Usage

set_read(file_name = "set_#NUM#.csv", path = ".", num = 1, sep = ",",
  dec = ".", cols = 0, rows = 0, additional_vars = vector(),
  additional_sep = "[^[:alnum:]]+")

Arguments

`file_name`	Name of the file from which to read the data. May contain "#NUM#" as a placeholder if you have multiple files.
`path`	The path to the file (no trailing "/" or "\" !).
`num`	Number of the set to read, inserted for "#NUM#".
`sep`	Separator used in the csv-file, either "," or ";" (see `utils::read.csv()`).
`dec`	The character used for decimal points (see `utils::read.csv()`). "AUTO" will result in "." if `sep` is "," and "," for ";".
`cols`	Number of columns in the input matrix (`0` means auto-detect).
`rows`	Number of rows containing values (not names / additional data) in the input matrix (`0` means auto-detect).
`additional_vars`	Vector of strings containing the names for the additional columns.
`additional_sep`	String / RegExp that separates additional vars, e.g.: `"ID_blue_cold"` with `additional_sep = "_"` will be separated into three columns containing `"ID"`, `"blue"` and `"cold"`. If the separated data would exceed the columns in `additional_vars` the last column will contain a string with separator (e.g.: `"blue_cold"`). If data is missing `NA` is inserted.

Value

A tibble containing (at minimum) set, position, sample_id, name and value.

Examples

# a file containing only values
read.csv(
  file = system.file("extdata", "values.csv", package = "bioset"),
  header = FALSE,
  colClasses = "character"
)

# read into a tibble
set_read(
  file_name = "values_names.csv",
  path = system.file("extdata", package = "bioset"),
)

# file containing names
read.csv(
  file = system.file("extdata", "values_names.csv", package = "bioset"),
  header = FALSE,
  colClasses = "character"
)

# read a file containing labels and store those in column "name"
set_read(
  file_name = "values_names.csv",
  path = system.file("extdata", package = "bioset"),
  additional_vars = c("name")
)

# file with names and properties
read.csv(
  file = system.file(
    "extdata", "values_names_properties.csv", package = "bioset"),
  header = FALSE,
  colClasses = "character"
)

# read a file containing labels and properties and store those in columns
# "name" and "time"
# splits names by every character that's not A-Z, a-z, 0-9
# to change that behaviour use additional_sep
set_read(
  file_name = "values_names_properties.csv",
  path = system.file("extdata", package = "bioset"),
  additional_vars = c("name", "time")
)

# read file "set_1.csv" containing labels
set_read(
  num = 1,
  path = system.file("extdata", package = "bioset"),
  additional_vars = c("name", "time")
)

# read file "set_2.csv" containing labels
set_read(
  num = 2,
  path = system.file("extdata", package = "bioset"),
  additional_vars = c("name", "time")
)

# read file "plate_2.csv" containing labels
set_read(
  num = 2,
  file_name = "plate_#NUM#.csv",
  path = system.file("extdata", package = "bioset"),
  additional_vars = c("name", "time")
)