Read Biotek Output CSV Files

Read Biotek Output CSV Files

Usage

plate_read_biotek(file, time_average = TRUE, second_wl = FALSE, plate = NULL)

Arguments

file

The filepath to a .csv file, exported from a Biotek plate reader.

time_average

Logical, whether to average the time points across different observations (LUM / OD) and pivot them to their own columns.

second_wl

Whether to include the second wavelength when reading in data blocks, or to keep just the label and the first wavelength.

plate

The size of the plate, such as 96 or 384, or its number of rows and columns. If NULL, the plate size recorded in the file is used, or else the smallest standard plate that holds all the wells.

Value

A tibble. The well column holds well() IDs that know the size of the plate.

Examples

file_data <- system.file(
  "extdata",
  "2024-02-29_vio_GFP_main.csv",
  package = "wellr"
)

plate_read_biotek(file_data)
#> # A tibble: 14,304 × 7
#>     time well      od600 gfp_485 vio_575 vio_585 vio_595
#>    <dbl> <well:96> <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
#>  1  469. A01       0.041     260   0.042   0.041   0.041
#>  2  469. A02       0.043     258   0.044   0.044   0.043
#>  3  469. A03       0.043     258   0.044   0.044   0.044
#>  4  469. A04       0.044     254   0.044   0.044   0.044
#>  5  469. A05       0.044     256   0.044   0.044   0.044
#>  6  469. A06       0.043     255   0.044   0.044   0.044
#>  7  469. A07       0.043     244   0.044   0.044   0.044
#>  8  469. A08       0.045     252   0.045   0.045   0.045
#>  9  469. A09       0.045     251   0.045   0.045   0.045
#> 10  469. A10       0.045     247   0.045   0.046   0.045
#> # ℹ 14,294 more rows
plate_read_biotek(file_data, second_wl = TRUE)
#> # A tibble: 14,304 × 7
#>     time well      od600 gfp_485_530 vio_575 vio_585 vio_595
#>    <dbl> <well:96> <dbl>       <dbl>   <dbl>   <dbl>   <dbl>
#>  1  469. A01       0.041         260   0.042   0.041   0.041
#>  2  469. A02       0.043         258   0.044   0.044   0.043
#>  3  469. A03       0.043         258   0.044   0.044   0.044
#>  4  469. A04       0.044         254   0.044   0.044   0.044
#>  5  469. A05       0.044         256   0.044   0.044   0.044
#>  6  469. A06       0.043         255   0.044   0.044   0.044
#>  7  469. A07       0.043         244   0.044   0.044   0.044
#>  8  469. A08       0.045         252   0.045   0.045   0.045
#>  9  469. A09       0.045         251   0.045   0.045   0.045
#> 10  469. A10       0.045         247   0.045   0.046   0.045
#> # ℹ 14,294 more rows