Calculate differential abundance between conditions

Source: R/calculate_diff_abundance.R

[Deprecated] This function was deprecated due to its name changing to calculate_diff_abundance().

diff_abundance(...)

Value

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.