Perform differential protein expression analysis

Usage

get_DEPresults(
  se,
  condition1 = NULL,
  condition2 = NULL,
  ref_condition = NULL,
  tests = NULL,
  alpha = 0.05,
  lfc = 1,
  type = "manual",
  fdr_type = "BH"
)

Arguments

se: SummarizedExperiment object with protein expression data.
condition1: One of the conditions to be tested present in expDesign.
condition2: One of the conditions to be tested present in expDesign.
ref_condition: One of the conditions in expDesign that is used as reference. Must be used in combination with type = 'control'.
tests: Character vector specifying which contrasts to test when using "type = 'manual'"
alpha: the p.adjust significance cutoff.
lfc: The log2 fold change significance cutoff.
type: Type of comparison to be made. Options are: 'manual', 'control', and 'all'.
fdr_type: Type of fdr correction. Options are 'fdrtool' and 'BH' (Benjamini-Hochberg). Default is 'BH'

Value

A data frame with the results of differential protein expression analysis

Examples

se <- prepare_se(report.pg_matrix, expDesign)

#> Imputing along margin 2 (samples/columns).
#> [1] 0.3066195
#> Imputing along margin 1 (features/rows).
#> Warning: 36 rows with more than 50 % entries missing;
#>  mean imputation used for these rows
#> Cluster size 5574 broken into 3662 1912 
#> Cluster size 3662 broken into 1462 2200 
#> Done cluster 1462 
#> Cluster size 2200 broken into 1110 1090 
#> Done cluster 1110 
#> Done cluster 1090 
#> Done cluster 2200 
#> Done cluster 3662 
#> Cluster size 1912 broken into 1379 533 
#> Done cluster 1379 
#> Done cluster 533 
#> Done cluster 1912 
res <- get_DEPresults(se, 'motif1', 'neg_ctrl', type = 'manual')
#> Tested contrasts: motif1_vs_neg_ctrl