dmrscaler: dmrscaler

In leroybondhus/dmrscaler: What the Package Does (One Line, Title Case)

dmrscaler

Description

dmrscaler

dmrscaler

Usage

dmrscaler(
  locs,
  locs_pval_cutoff = 0.05,
  region_signif_method = c("bonferroni", "benjamini-yekutieli", "p-value"),
  region_signif_cutoff = 0.01,
  window_type = c("k_nearest", "genomic_width"),
  window_sizes = c(2, 4, 8, 16, 32, 64),
  dmr_constraint_list = NULL,
  output_type = c("simple", "complete")
)

dmrscaler(
  locs,
  locs_pval_cutoff = 0.05,
  region_signif_method = c("bonferroni", "benjamini-yekutieli", "p-value"),
  region_signif_cutoff = 0.01,
  window_type = c("k_nearest", "genomic_width"),
  window_sizes = c(2, 4, 8, 16, 32, 64),
  dmr_constraint_list = NULL,
  output_type = c("simple", "complete")
)

Arguments

locs	dataframe of measured CpG loci with columns as "chr", "pos", "pval"
region_signif_method	one of "p-value" or "benjamini-yekutieli" (false discovery rate control) or "bonferroni" (family-wise error rate)
region_signif_cutoff	p-value or fwer at which regions are considered significant or desired fdr is achieved for regions
window_type	specifies one of "k_nearest" or "genomic_width"
window_sizes	vector of window size for each layer where window_type determines whether this represents the genomic_width of windows or the k_nearest neighbors that compose a window
dmr_constraint_list	(ADD LATER)(optional) a list of rules that further constrains the definition of a differentially methylated region
output_type	one of "simple" or "complete" where "simple" returns only the topmost layer as a dataframe of dmrs and "complete" returns a list of dataframes of dmrs that were called at and/or propegated up through each layer
loc_signif_method	one of "p-value" or "fdr" (false discovery rate)
loc_signif_cutoff	p-value at which individual CpGs are considered significant or desired fdr is achieved for individual CpGs

Value

dmrscaler returns a list of dmrs at each layer

dmrscaler returns a list of dmrs at each layer

leroybondhus/dmrscaler documentation built on July 11, 2022, 4:56 a.m.