dot-find_dmrs: Finding differentially methylated regions

In stephaniehicks/methylCC: Estimate the cell composition of whole blood in DNA methylation samples

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.