Relabel the significance column in the DEP results data frame

Usage

recode_sig_col(res, pval_cutoff = 0.05, fc_cutoff = 1)

Arguments

res: Results data frame after DEP analysis.
pval_cutoff: The p.adj significance cutoff
fc_cutoff: The absolute log2 fold change significance cutoff

Value

The results data frame with adjusted significance column

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, type = 'all')
#> Tested contrasts: neg_ctrl_vs_motif1, neg_ctrl_vs_motif2, motif1_vs_motif2
res <- recode_sig_col(res, pval_cutoff = 0.01, fc_cutoff = 1)