empirical_pval {DAMEfinder} | R Documentation |
This function permutes the coefficient of interest and re-runs
get_tstats
and regionFinder
for each permutation.
Code for permutations copied from the dmrseq
function from the package
of the same name.
empirical_pval( presa, design, rforiginal, coeff, cont, smooth, maxPerms = 10, Q, maxGap, method, ... )
presa |
SExperiment output from |
design |
design matrix. |
rforiginal |
data.frame of DAMEs calculated with original design. |
coeff |
Coefficient of interest to permute. |
cont |
same as in |
smooth |
Boolean. |
maxPerms |
Maximum possible permutations generated. Default = 10. |
Q |
Quantile for cuttof. |
maxGap |
Same as other functions in the package. |
method |
lmFit method. |
... |
Passed to |
Vector of empirical p-values.