.find_dmrs {methylCC} | R 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.

[Package methylCC version 1.0.0 Index]