dot-find_dmrs: Finding differentially methylated regions

.find_dmrsR Documentation

Finding differentially methylated regions

Description

This function uses the FlowSorted.Blood.450k whole blood reference methylomes with six cell types to identify differentially methylated regions.

Usage

.find_dmrs(verbose = TRUE, gr_target = NULL, include_cpgs = FALSE,
  include_dmrs = TRUE, num_cpgs = 50, num_regions = 50,
  bumphunter_beta_cutoff = 0.2, dmr_up_cutoff = 0.5,
  dmr_down_cutoff = 0.4, dmr_pval_cutoff = 1e-11,
  cpg_pval_cutoff = 1e-08, cpg_up_dm_cutoff = 0,
  cpg_down_dm_cutoff = 0, pairwise_comparison = FALSE,
  mset_train_flow_sort = NULL)

Arguments

verbose

TRUE/FALSE argument specifying if verbose messages should be returned or not. Default is TRUE.

gr_target

Default is NULL. However, the user can provide a GRanges object from the object in estimatecc. Before starting the procedure to find differentially methylated regions, the intersection of the gr_target and GRanges object from the reference methylomes (FlowSorted.Blood.450k).

include_cpgs

TRUE/FALSE. Should individual CpGs be returned. Default is FALSE.

include_dmrs

TRUE/FALSE. Should differentially methylated regions be returned. Default is TRUE. User can turn this to FALSE and search for only CpGs.

num_cpgs

The max number of CpGs to return for each cell type. Default is 50.

num_regions

The max number of DMRs to return for each cell type. Default is 50.

bumphunter_beta_cutoff

The cutoff threshold in bumphunter() in the bumphunter package.

dmr_up_cutoff

A cutoff threshold for identifying DMRs that are methylated in one cell type, but not in the other cell types.

dmr_down_cutoff

A cutoff threshold for identifying DMRs that are not methylated in one cell type, but methylated in the other cell types.

dmr_pval_cutoff

A cutoff threshold for the p-values when identifying DMRs that are methylated in one cell type, but not in the other cell types (or vice versa).

cpg_pval_cutoff

A cutoff threshold for the p-values when identifying differentially methylated CpGs that are methylated in one cell type, but not in the other cell types (or vice versa).

cpg_up_dm_cutoff

A cutoff threshold for identifying differentially methylated CpGs that are methylated in one cell type, but not in the other cell types.

cpg_down_dm_cutoff

A cutoff threshold for identifying differentially methylated CpGs that are not methylated in one cell type, but are methylated in the other cell types.

pairwise_comparison

TRUE/FAlSE of whether all pairwise comparisons (e.g. methylated in Granulocytes and Monocytes, but not methylated in other cell types). Default if FALSE.

mset_train_flow_sort

Default is NULL. However, a user can provide a MethylSet object after processing the FlowSorted.Blood.450k dataset. The default normalization is preprocessIllumina().

Value

A list of data frames and GRanges objects.


stephaniehicks/methylCC documentation built on Nov. 6, 2022, 5:51 p.m.