Performing ROTS
Usage
perform_ROTS(
data,
condition,
comparisons,
condition_name,
coldata,
logFC = TRUE,
logFC_up = 1,
logFC_down = -1,
p_adj = TRUE,
alpha = 0.05,
B = 100,
K = 500
)Arguments
- data
Data table of intensities (rows = proteins, cols = samples)
- condition
Vector of experimental design specifying the condition(s) to compare
- comparisons
Vector of comparisons that are performed in the DE analysis (from specify_comparisons method)
- condition_name
String of name of condition in colData
- coldata
colData of the SummarizedExperiment
- 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