Add known concentrations of protein to standard samples

Usage

qp_add_std_conc(x, standard_scale = c(0, 2^((2:7) - 5)), ...)

# S3 method for data.frame
qp_add_std_conc(x, standard_scale = c(0, 2^((2:7) - 5)), ...)

# S3 method for list
qp_add_std_conc(x, standard_scale = c(0, 2^((2:7) - 5)), ...)

Arguments

x: A data.frame containing a sample_type and index columns. See details.
standard_scale: A numeric vector giving the concentrations of the standards. The units are arbitrary, but will determine the units of the output concentrations.
...: Unused

Value

Same type as x, with a .conc column

Details

Input is expected to have two columns:

sample_type: A character vector denoting which samples are standards with "standard". All other values will be considered unknowns.
index: A numeric column denoting the sample number. Index 1 will correspond to the first item in standard_scale, 2 will be the second, etc.

Examples

abs <- expand.grid(
  sample_type = c("standard", "unknown"),
  index = 1:7
)

abs
#>    sample_type index
#> 1     standard     1
#> 2      unknown     1
#> 3     standard     2
#> 4      unknown     2
#> 5     standard     3
#> 6      unknown     3
#> 7     standard     4
#> 8      unknown     4
#> 9     standard     5
#> 10     unknown     5
#> 11    standard     6
#> 12     unknown     6
#> 13    standard     7
#> 14     unknown     7

qp_add_std_conc(abs)
#>    sample_type index .conc
#> 1     standard     1 0.000
#> 3     standard     2 0.125
#> 5     standard     3 0.250
#> 7     standard     4 0.500
#> 9     standard     5 1.000
#> 11    standard     6 2.000
#> 13    standard     7 4.000
#> 2      unknown     1    NA
#> 4      unknown     2    NA
#> 6      unknown     3    NA
#> 8      unknown     4    NA
#> 10     unknown     5    NA
#> 12     unknown     6    NA
#> 14     unknown     7    NA

# Can add custom scale - doesn't have to be 'in order' or unique:
qp_add_std_conc(abs, c(1, 4, 2, 2, 3, 0.125, 7))
#>    sample_type index .conc
#> 1     standard     1 1.000
#> 3     standard     2 4.000
#> 5     standard     3 2.000
#> 7     standard     4 2.000
#> 9     standard     5 3.000
#> 11    standard     6 0.125
#> 13    standard     7 7.000
#> 2      unknown     1    NA
#> 4      unknown     2    NA
#> 6      unknown     3    NA
#> 8      unknown     4    NA
#> 10     unknown     5    NA
#> 12     unknown     6    NA
#> 14     unknown     7    NA

# Will warn - more values in `standard_scale` than standard indices
# Will drop extra
qp_add_std_conc(abs, 1:8)
#> Warning: Not all standards in scale used
#>    sample_type index .conc
#> 1     standard     1     1
#> 3     standard     2     2
#> 5     standard     3     3
#> 7     standard     4     4
#> 9     standard     5     5
#> 11    standard     6     6
#> 13    standard     7     7
#> 2      unknown     1    NA
#> 4      unknown     2    NA
#> 6      unknown     3    NA
#> 8      unknown     4    NA
#> 10     unknown     5    NA
#> 12     unknown     6    NA
#> 14     unknown     7    NA

# Will error - fewer values in `standard_scale` than standard indices
if (FALSE) {
  qp_add_std_conc(abs, 1:6)
}