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Create p-value dataset

calculate_p_value.Rd

Create p-value dataset

Usage

calculate_p_value(
  dat,
  protein = unique(dat[["Protein"]])[1],
  state_1 = unique(dat[["State"]])[1],
  state_2 = unique(dat[["State"]])[2],
  p_adjustment_method = "none",
  confidence_level = 0.98
)

Arguments

dat

data imported by the read_hdx function.

protein

chosen protein.

state_1

biological state for chosen protein. From this state values the second state values are subtracted to get the deuterium uptake difference.

state_2

biological state for chosen protein. This state values are subtracted from the first state values to get the deuterium uptake difference.

p_adjustment_method

method of adjustment P-values for multiple comparisons. Possible methods: "BH" (Benjamini & Hochberg correction), "bonferroni" (Bonferroni correction) and "none" (default).

confidence_level

confidence level for the t-test.

Value

a data.frame object.

Details

This function calculates P-value based on the supplied data. Unpaired t-Student test (with supplied parameters) is used to establish if the null hypothesis (there is no difference between measured mass values between two selected biological states) can be rejected, based on the experimental mass values from replicates of the experiment - for peptide in given time point of measurement. For the peptides that have only one replicate of the measurement (in any state) the P-value cannot be calculated and is assigned with NA value.

See also

read_hdx calculate_exp_masses_per_replicate plot_volcano create_diff_uptake_dataset create_p_diff_uptake_dataset

Examples

p_dat <- calculate_p_value(alpha_dat)
head(p_dat)
#>      Protein    Sequence Exposure Modification Start   End     P_value
#>       <char>      <char>    <num>       <lgcl> <int> <int>       <num>
#> 1: db_eEF1Ba GFGDLKSPAGL    0.000           NA     1    11          NA
#> 2: db_eEF1Ba GFGDLKSPAGL    0.167           NA     1    11 0.065344248
#> 3: db_eEF1Ba GFGDLKSPAGL    1.000           NA     1    11 0.001789245
#> 4: db_eEF1Ba GFGDLKSPAGL    5.000           NA     1    11          NA
#> 5: db_eEF1Ba GFGDLKSPAGL   25.000           NA     1    11 0.023503782
#> 6: db_eEF1Ba GFGDLKSPAGL  150.000           NA     1    11 0.530754368
#>    log_p_value
#>          <num>
#> 1:          NA
#> 2:   2.7280859
#> 3:   6.3259618
#> 4:          NA
#> 5:   3.7505939
#> 6:   0.6334559