MSigDB_enrichment: Get enrichment with Molecular Signatures Database (MSigDB)

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

Get enrichment with Molecular Signatures Database (MSigDB)

Description

Get enrichment with Molecular Signatures Database (MSigDB c2 - v7p1). This function gets MSigDB enrichment and save the results in _mysmeth sufix. Data from : Walter and Eliza Hall Institute website for local bioinformatic resources. (http://bioinf.wehi.edu.au/MSigDB/v7.1/)

Usage

MSigDB_enrichment(
  data,
  out,
  filename,
  artype = "450K",
  bn = FALSE,
  fdr = NA,
  pval = NA,
  all = 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 _MSigDBif we are enriching a CpG vector _MSigDB_BNif we are enriching CpGs that meet the bonferroni condition _MSigDB_FDRif we are enriching CpGs that meet the FDR condition _MSigDB_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

Value

A list with resulth enriched data. Results also are stored in a folder MSigDB inside Enrichment default path

isglobal-brge/EASIER documentation built on Feb. 12, 2024, 6:30 p.m.