runBumphunter {MEAL} | R Documentation |
Run bumphunter to a methylation dataset. This function contains all steps of bumphunter analysis, from model.matrix creation to running the analysis.
runBumphunter(set, model, coefficient = 2, bumphunter_cutoff = 0.1, num_permutations = 0, bumps_max = 30000, betas = TRUE, check_perms = FALSE, verbose = FALSE, resultSet = FALSE, ...)
set |
|
model |
Model matrix or formula to get model matrix from |
coefficient |
Numeric with the column of model matrix used in the analysis. (Default: 2) |
bumphunter_cutoff |
Numeric with the minimum cutoff to include a probe in a block. (Default: 0.1) |
num_permutations |
Numeric with the number of permutations run to compute the bumps p-value. (Default: 0) |
bumps_max |
Numeric with the maximum number of bumps used in the permutation.
This parameter only applies when |
betas |
If |
check_perms |
Logical. Should we check that there are less bumps than
|
verbose |
Logical value. Should the function be verbose? (Default: FALSE) |
resultSet |
Should results be encapsulated in a |
... |
Further arguments passed to |
runBumphunter is a wrapper for minfi bumphunter
. This function
runs all the steps required prior running bumphunter from the methylation set
and the formula of the model. This implementation allows running bumphunter to other
objects than GenomicRatioSet
. The result can be encapsulated in a
ResultSet
to take adavantege of its plotting capabilities.
If the user wants to run permutations to calculate p-values, this implementation
can filter the bumps to avoid doing a very high number of permutations and to
reduce computation time. To do so, we can set the maximum number of bumps that
we want to permute with the bumps_max
parameter. runBumphunter increases
bumphunter_cutoff
value until the number of bumps is lower than
bumps_max
.
data.frame or resultSet
with the result of bumphunter