View source: R/epi_parameters.R
epi_parameters | R Documentation |
epimutations
and epimutations_one_leave_out
functionsAllow the user to set the values of the parameters to compute the functions epimutations and epimutations_one_leave_out.
epi_parameters(
manova = list(pvalue_cutoff = 0.05),
mlm = list(pvalue_cutoff = 0.05),
iForest = list(outlier_score_cutoff = 0.7, ntrees = 100),
mahdist = list(nsamp = "deterministic"),
quantile = list(window_sz = 1000, offset_abs = 0.15, qsup = 0.995, qinf = 0.005),
beta = list(pvalue_cutoff = 1e-06, diff_threshold = 0.1)
)
manova , mlm , iForest , mahdist , quantile , beta |
method selected in the function epimutations. |
pvalue_cutoff |
the threshold p value to select
which CpG regions are outliers in |
outlier_score_cutoff |
The outlier score
threshold to identify outliers CpGs in
isolation forest ( |
ntrees |
number of binary trees to build for the model build by
isolation forest ( |
nsamp |
the number of subsets used for initial
estimates in the Minimum Covariance Determinant
which is used to compute the Robust Mahalanobis
distance ( |
window_sz |
the maximum distance between
CpGs to be considered in the same DMR.
This parameter is used in |
qsup , qinf , offset_abs |
The upper and lower quantiles (threshold)
to consider a CpG an outlier when using |
diff_threshold |
Minimum methylation difference between the CpG and the mean methylation to consider a position an outlier. |
Invoking epi_parameters()
with
no arguments returns return a list with the default values.
the function returns a list of all set parameters for each method used in epimutations and epimutations_one_leave_out functions.
#Default set of parameters
epi_parameters()
#change p value for manova method
epi_parameters(manova = list("pvalue_cutoff" = 0.01))
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