meth_bootstrap: Bootstrapped randomly samples values

In methcon5: Identify and Rank CpG DNA Methylation Conservation Along the Human Genome

Description

"perm_v1" (the default method) will sample the variables the rows independently. "perm_v2" will sample regions of same size while allowing overlap between different regions. "perm_v3" will sample regions under the constraint that all sampled regions are contained in the region they are sampled in.

Usage

meth_bootstrap(data, reps, method = c("perm_v1", "perm_v2", "perm_v3"))

Arguments

data	a methcon data.frame output from 'meth_bootstrap'.
reps	Number of reps, defaults to 1000.
method	Character, determining which method to use. See details for information about methods. Defaults to "perm_v1".

Details

Note that you can apply 'meth_bootstrap' multiple times to get values for different methods.

Value

A methcon object. Contains the aggregated data along with original data.frame and variable selections and bootstrapped values.

Examples

# Note that you likely want to do more than 10 repitions.
# rep = 10 was chosen to have the examples run fast.

fake_methylation %>%
  meth_aggregate(id = gene, value = meth, fun = mean) %>%
  meth_bootstrap(10)

fake_methylation %>%
  meth_aggregate(id = gene, value = meth, fun = mean) %>%
  meth_bootstrap(10, method = "perm_v2")

# Get multiple bootstraps
fake_methylation %>%
  meth_aggregate(id = gene, value = meth, fun = mean) %>%
  meth_bootstrap(10, method = "perm_v1") %>%
  meth_bootstrap(10, method = "perm_v2") %>%
  meth_bootstrap(10, method = "perm_v3")

methcon5 documentation built on Jan. 11, 2020, 9:39 a.m.