Get properties of an FP from FPbase

Gets properties of an FP from FPbase, including the maximal excitation wavelength and extinction coefficient. Optionally saves these as a CSV.

Usage

get_fpbase_properties(
  slug,
  verbose = TRUE,
  save_file = FALSE,
  outfolder = ".",
  filename = "fp_properties.csv"
)

Arguments

slug

Name of FP, which is used to find the FP-relevant data lines in the FPbase datasets. This argument is called slug because for FPbase retrievals, this needs to be an exact match to the slug specified by FPbase. (To find this, navigate to the FPbase entry for your FP and copy the part after https://www.fpbase.org/protein/ (without the trailing /).

verbose

logical. Should the function print messages to allow the user to check its progress? Defaults to TRUE.

save_file

logical. Should the function save the output as a CSV file? Defaults to FALSE.

outfolder

path to folder where output files should be saved. Defaults to current working directory.

filename

How to name the output CSV file. Requires .csv at the end. Defaults to fp_properties.csv.

Examples

get_fpbase_properties("mcherry")
#> FP data retrieved from FPbase.
#>              slug    name ex_max em_max ext_coeff   qy pka maturation lifetime
#> 1 mcherry_default default    587    610     72000 0.22 4.5         15      1.4
#>   brightness
#> 1      15.84