Run DE analysis of a selection of normalized data sets

Usage

run_DE(
  se,
  comparisons,
  ain = NULL,
  condition = NULL,
  DE_method = "limma",
  covariate = NULL,
  logFC = TRUE,
  logFC_up = 1,
  logFC_down = -1,
  p_adj = TRUE,
  alpha = 0.05,
  B = 100,
  K = 500,
  trend = TRUE,
  robust = TRUE
)

Arguments

se: SummarizedExperiment containing all necessary information of the proteomics data set
comparisons: Vector of comparisons that are performed in the DE analysis (from specify_comparisons method)
ain: Vector of strings which assay should be used as input (default NULL). If NULL then all normalization of the se object are plotted next to each other.
condition: column name of condition (if NULL, condition saved in SummarizedExperiment will be taken)
DE_method: String specifying which DE method should be applied (limma, ROTS)
covariate: String specifying which column to include as covariate into limma
logFC: Boolean specifying whether to apply a logFC threshold (TRUE) or not (FALSE)
logFC_up: Upper log2 fold change threshold (dividing into up regulated)
logFC_down: Lower log2 fold change threshold (dividing into down regulated)
p_adj: Boolean specifying whether to apply a threshold on adjusted p-values (TRUE) or on raw p-values (FALSE)
alpha: Threshold for adjusted p-values or p-values
B: Number of bootstrapping for ROTS
K: Number of top-ranked features for reproducibility optimization
trend: logical, should an intensity-dependent trend be allowed for the prior variance? If FALSE then the prior variance is constant. Alternatively, trend can be a row-wise numeric vector, which will be used as the covariate for the prior variance.
robust: logical, should the estimation of df.prior and var.prior be robustified against outlier sample variances?

Value

Data table of DE results of selected normalized data sets

Examples

data(tuberculosis_TMT_se)
comparisons <- specify_comparisons(tuberculosis_TMT_se, condition = NULL,
                            sep = NULL, control = NULL)
#> Condition of SummarizedExperiment used!
de_res <- run_DE(tuberculosis_TMT_se, comparisons,
              ain = NULL, condition = NULL, DE_method = "limma",
              logFC = TRUE, logFC_up = 1, logFC_down = -1, p_adj = TRUE,
              alpha = 0.05, B = 100, K = 500, trend = TRUE, robust = TRUE)
#> Condition of SummarizedExperiment used!
#> All assays of the SummarizedExperiment will be used.
#> DE Analysis will not be performed on raw data.
#> Warning: Partial NA coefficients for 114 probe(s)
#> log2: DE analysis completed.
#> Warning: Partial NA coefficients for 114 probe(s)
#> RobNorm: DE analysis completed.
#> Warning: Partial NA coefficients for 112 probe(s)
#> IRS_on_RobNorm: DE analysis completed.
#> Warning: Partial NA coefficients for 114 probe(s)
#> Median: DE analysis completed.
#> Warning: Partial NA coefficients for 112 probe(s)
#> IRS_on_Median: DE analysis completed.