Perform DEqMS
Usage
perform_DEqMS(
fit,
se,
DEqMS_PSMs_column = NULL,
logFC = TRUE,
logFC_up = 1,
logFC_down = -1,
p_adj = TRUE,
alpha = 0.05
)Arguments
- fit
eBayes object resulting from perform_limma method
- se
SummarizedExperiment containing all necessary information of the proteomics data set
- DEqMS_PSMs_column
String specifying which column name to use for DEqMS (default NULL). Any column of the rowData(se) is accepted.
- 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