Title: Cleans and normalizes DAT files obtained from experiments using the FLUOstar Omega microplate reader (from BMG LABTECH).

The simplest case scenario entails inputting the name or directory of a DAT file as a string, the number of rows denoted by the tnp (test, negative, positive) parameter, and the number of cycles (selected by the user when running the FLUOstar instrument). The program takes these three baseline parameters, performs cleaning and normalization of the DAT file, and then appends an attribute called “Cycle_Number” to the normalized data frame.

Usage

normfluordat(
  dat,
  tnp,
  cycles,
  rows_used = NULL,
  cols_used = NULL,
  user_specific_labels = NULL,
  read_direction = NULL,
  na_omit = NULL
)

Arguments

dat: A string ("dat_1.dat") if the file is found within the present working directory (pwd) OR a path pointing directly to a ".dat" file.
tnp: A numeric value indicating the number of rows used. TNP is used as an acronym for Test, Negative, Positive.
cycles: A numeric value indicating the number of cycles selected by the user when running the FLUOstar instrument.
rows_used: A character vector of the rows used; ru = c('A','B','C').
cols_used: A numeric vector of the columns used; cu = c(1,2,3).
user_specific_labels: A character vector manually prepared by the user to denote the wells used on the microplate reader; usl = c('A1','B1','C1').
read_direction: A string input with two choices, “vertical” or “horizontal.” The user indicates “vertical” if the user intends to have a final data frame with samples arranged as sample type triplets (A1, B1, C1, A1, B1, C1) OR “horizontal” if the user intends to have a final data frame with samples.
na_omit: Takes a string "yes" OR "no".

Value

A normalized data frame with an appended "Cycle_Number" attribute. The “Cycle_Number” attribute is the X-variable.

Note

This function has less optimized space and time complexities than @seealso normfluodat(). In real-time the difference in optimization is not noticeable. This function also takes less parameters than the more optimized version of the function. Use @seealso normfluodat() for better approximation of attribute names.

Author

Tingwei Adeck

Examples

fpath <- system.file("extdata", "dat_1.dat", package = "normfluodbf", mustWork = TRUE)
normalized_fluo_dat <- normfluordat(dat=fpath, tnp = 3, cycles = 40)
#> The User is advised to input a character vector of rows used
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 1
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 4
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 5
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 6
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 7
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 8
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 10
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 11
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 12
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 13
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 14
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 17
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 18
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 20
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 21
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 22
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 23
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 24
#> 🐷🐫
#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 25
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 26
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 27
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 28
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 29
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 30
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 31
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 32
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 33
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#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 34
#> 🐷🐫
#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 35
#> 🐷🐫
#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 36
#> 🐷🐫
#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 37
#> 🐷🐫
#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 38
#> 🐷🐫
#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 39
#> 🐷🐫
#> YIKES, value < 2^11, Watch in future experimental designs column: 27 row: 40