Description Usage Arguments Details Value Author(s) Examples
Get correlated regions with significant correlations
1 2 3 | filter_correlated_regions(chromosome = paste0("chr", 1:22), template,
cutoff = 0.05, adj_method = "BH", meth_diameter_cutoff = 0.25, meth_IQR_cutoff = 0.25,
anova_cutoff = 0.05)
|
chromosome |
a vector of chromosome names |
template |
template path to find cr files |
cutoff |
cutoff of adjusted correlation p-values |
adj_method |
method for calculating adjusted p-values |
meth_diameter_cutoff |
cutoff for methylation diameters |
meth_IQR_cutoff |
cutoff for IQR, if there is no subtype information, IQR is used to remove less variable methylation |
anova_cutoff |
cutoff for adjust ANOVA p-values |
As explained in correlated_regions
, original cr is huge and is always saved as a separated file for single chromosome.
Here template
defined how to get the cr files. E.g. if template
is defined as "path_to/@chr_cr.rds", the funciton
will replace "@chr" to every chromosome and read the data.
Two additional columns are attached:
FDR for correlation p-values
FDR for anova test, will be added only if factor
is set in correlated_regions
.
A GRanges
object
Zuguang Gu <z.gu@dkfz.de>
1 2 | # There is no example
NULL
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