Chromatin_enrichment: Get enrichment with Chromatin State and classify hypo i...

In isglobal-brge/EASIER: EwAS: quality control, meta-analysIs and EnRichment

Get enrichment with Chromatin State and classify hypo i hypermethylation states

Description

Get enrichment with Chromatin States Database (chrom15). This function gets Chromatin states and creates a field meth_level for hypo and Hypermethylation states if beta field is found, if not, only enrichment is performed.

Usage

Chromatin_enrichment(
  data,
  out,
  filename,
  cpgcol,
  bn = FALSE,
  fdr = NA,
  pval = NA,
  all = FALSE
)

Arguments

data	array or dataframe with CpGs to perform enrichment. If not beta field found then hypo and hypermethylation field is added
out	string, Path where the results should be saved
filename	string, File name where the results should be saved, to this name the suffix is added depending on data to enrich _chrom15if we are enriching a CpG vector _chrom15_BNif we are enriching CpGs that meet the bonferroni condition _chrom15_FDRif we are enriching CpGs that meet the FDR condition _chrom15_PVALif we are enriching CpGs that meet the p-value condition
cpgcol	numeric or string. Column index or column name with CpGs id
bn	boolean. optional. If data is a dataframe with bonferroni adjustment, makes enrichment with CpGs that pass Bonferroni
fdr	numeric optiona. If data is a dataframe with FDR adjustment and fdr!=NA or NULL, makes enrichment with CpGs with fdr lower than indicated value
pval	numeric optional. If data is a dataframe with p-value and pval!=NA or NULL, makes enrichment with CpGs with pval lower than indicated value
all	boolean, optional. enrich all CpGs

Value

A list with resulth enriched data.

isglobal-brge/EASIER documentation built on Sept. 25, 2024, 10:50 p.m.