missMethyl_enrichment: Get Pathways enrichment with missMethyl

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

Get Pathways enrichment with missMethyl

Description

Get Pathways enrichment with missMethyl Bioconductor package. This function gets GO enrichment and KEGG enrichment from input data and save the results in a two separated files, one with GO enrichment and the other with KEGG enrichment with _GO and _KEGG sufix respectively.

Usage

missMethyl_enrichment(
  data,
  out,
  filename,
  artype = "450K",
  bn = FALSE,
  fdr = NA,
  pval = NA,
  all = FALSE,
  outputdir = NULL,
  plots = FALSE
)

Arguments

data	array or dataframe with CpGs to perform enrichment. Dataframe option is used to filter by Bonferroni FDR or p-value, in order to filter by this fields, function needs that Bonferroni with adjustments field to be called "Bonferroni", the field with the FDR adjustments to be called FDR and the field with the p-value to be called p.value
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 _mysmethif we are enriching a CpG vector _mysmeth_BNif we are enriching CpGs that meet the bonferroni condition _mysmeth_FDRif we are enriching CpGs that meet the FDR condition _mysmeth_PVALif we are enriching CpGs that meet the p-value condition
artype	string, Illumina array type, 450K or EPIC, by default array type is 450K
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
plots	boolean, optional. generate plots with GO and KEGG data

Value

File with descriptive and plots from MyssMethyl results. Results are stored in a folder MyssMethyl inside Enrichment default path

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