`R/calculate_diff_abundance.R`

`diff_abundance.Rd`

This function was deprecated due to its name changing to `calculate_diff_abundance()`

.

`diff_abundance(...)`

A data frame that contains differential abundances (`diff`

), p-values (`pval`

)
and adjusted p-values (`adj_pval`

) for each protein, peptide or precursor (depending on
the `grouping`

variable) and the associated treatment/reference pair. Depending on the
method the data frame contains additional columns:

"t-test": The

`std_error`

column contains the standard error of the differential abundances.`n_obs`

contains the number of observations for the specific protein, peptide or precursor (depending on the`grouping`

variable) and the associated treatment/reference pair."t-test_mean_sd": Columns labeled as control refer to the second condition of the comparison pairs. Treated refers to the first condition.

`mean_control`

and`mean_treated`

columns contain the means for the reference and treatment condition, respectively.`sd_control`

and`sd_treated`

columns contain the standard deviations for the reference and treatment condition, respectively.`n_control`

and`n_treated`

columns contain the numbers of samples for the reference and treatment condition, respectively. The`std_error`

column contains the standard error of the differential abundances.`t_statistic`

contains the t_statistic for the t-test."moderated_t-test":

`CI_2.5`

and`CI_97.5`

contain the 2.5% and 97.5% confidence interval borders for differential abundances.`avg_abundance`

contains average abundances for treatment/reference pairs (mean of the two group means).`t_statistic`

contains the t_statistic for the t-test.`B`

The B-statistic is the log-odds that the protein, peptide or precursor (depending on`grouping`

) has a differential abundance between the two groups. Suppose B=1.5. The odds of differential abundance is exp(1.5)=4.48, i.e, about four and a half to one. The probability that there is a differential abundance is 4.48/(1+4.48)=0.82, i.e., the probability is about 82% that this group is differentially abundant. A B-statistic of zero corresponds to a 50-50 chance that the group is differentially abundant.`n_obs`

contains the number of observations for the specific protein, peptide or precursor (depending on the`grouping`

variable) and the associated treatment/reference pair."proDA": The

`std_error`

column contains the standard error of the differential abundances.`avg_abundance`

contains average abundances for treatment/reference pairs (mean of the two group means).`t_statistic`

contains the t_statistic for the t-test.`n_obs`

contains the number of observations for the specific protein, peptide or precursor (depending on the`grouping`

variable) and the associated treatment/reference pair.