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Get properties of an FP from FPbase

Source: R/get_fpbase_properties.R
get_fpbase_properties.Rd

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.

filename

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

Value

data frame of fluorescent protein properties

Examples

get_fpbase_properties("mcherry")
#> Warning in call to FPbase:
#> <simpleWarning in open.connection(con, "rb"): URL 'https://www.fpbase.org/api/proteins/?format=json': Timeout of 60 seconds was reached>
#> FP data retrieved from FPbase data stored in package.
#>                 url    name stokes    slug  ipg_id agg ex_max em_max ext_coeff
#> 1 /protein/mcherry/ mCherry     23 mcherry 3838123   m    587    610     72000
#>     qy pka brightness bleach maturation lifetime cofactor
#> 1 0.22 4.5      15.84     68         15      1.4