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Differential uptake data with confidence

show_diff_uptake_data_confidence.Rd

Present differential deuterium uptake values in selected form, accompanied by the significance

Usage

show_diff_uptake_data_confidence(
  diff_uptake_dat,
  theoretical = FALSE,
  fractional = FALSE,
  confidence_level = 0.98,
  hybrid = FALSE
)

Arguments

diff_uptake_dat

data produced by create_diff_uptake_dataset function

theoretical

logical, indicator if values are calculated using theoretical controls

fractional

logical, indicator if values are shown in fractional form

confidence_level

confidence level for the test, from range [0, 1].

hybrid

logical, indicator if the hybrid testing was applied in diff_uptake_dat.

Value

a data.frame object

Details

The function show_uptake_data generates a subsets of the uptake dat based on selected parameters. It contains the information if the value is statistically significant at selected confidence level. The numerical values are rounded to 4 places. The names of columns are changed to user-friendly ones.

See also

create_diff_uptake_dataset plot_differential

Examples

dat <- read_hdx(system.file(package = "HaDeX", "HaDeX/data/KD_180110_CD160_HVEM.csv"))
#> [1] ""
diff_uptake_dat <- create_diff_uptake_dataset(dat)
show_diff_uptake_data_confidence(diff_uptake_dat)
#>       Protein        Sequence    ID Modification Start   End Exposure
#>        <char>          <char> <int>       <lgcl> <int> <int>    <num>
#>   1: db_CD160 INITSSASQEGTRLN     1           NA     1    15    0.001
#>   2: db_CD160 INITSSASQEGTRLN     1           NA     1    15    0.167
#>   3: db_CD160 INITSSASQEGTRLN     1           NA     1    15    1.000
#>   4: db_CD160 INITSSASQEGTRLN     1           NA     1    15    5.000
#>   5: db_CD160 INITSSASQEGTRLN     1           NA     1    15   25.000
#>  ---                                                                 
#> 283: db_CD160        FSHNEGTL    41           NA   125   132    1.000
#> 284: db_CD160        FSHNEGTL    41           NA   125   132    5.000
#> 285: db_CD160        FSHNEGTL    41           NA   125   132   25.000
#> 286: db_CD160        FSHNEGTL    41           NA   125   132  120.000
#> 287: db_CD160        FSHNEGTL    41           NA   125   132 1440.000
#>      Diff DU [Da] U(Diff DU) [Da] Valid At 0.98
#>             <num>           <num>        <lgcl>
#>   1:       0.0000          0.0000         FALSE
#>   2:       0.3189          0.0460          TRUE
#>   3:       0.3413          0.0969          TRUE
#>   4:       0.5490          0.0825          TRUE
#>   5:       0.6439          0.0549          TRUE
#>  ---                                           
#> 283:      -0.0731          0.0377          TRUE
#> 284:      -0.0177          0.0221          TRUE
#> 285:       0.0456          0.0247          TRUE
#> 286:       0.0818          0.0418          TRUE
#> 287:       0.0057          0.0477         FALSE