exclude_CpGs: Exclude CpGs

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

Exclude CpGs

Description

Filter 450K or EPIC methylation array with previously defined conditions (selected conditionsin config.r). In order to minimize data size we merge only the selected ethnic column

Usage

exclude_CpGs(
  cohort,
  cpgid,
  exclude,
  ethnic,
  artype = "450K",
  filename = NULL,
  fileresume = NULL
)

Arguments

cohort	Dataframe with data
cpgid	string with the column name that contains the CpGs identifiators.
ethnic	. Ethnicity, possible values : ” (for none ethnic filter), EUR, SAS, AMR, GWD, YRI, TSI, IBS, CHS, PUR, JPT, GIH, CH_B, STU, ITU, LWK, KHV, FIN, ESN, CEU, PJL, AC_B, CLM, CDX, GBR, BE_B, PEL, MSL, MXL, ASW or GLOBAL.
artype	default value '450K'. Array type Illumina 450K or Illumina EPIC arrays, possible values are '450K' or 'EPIC' respectively.
filename	Optional, filename to write excluded cpgs and related information, if NULL no data are writed in a file
fileresume	Optional, filename to write descriptives for removed cpgs, if NULL no data are writed in a file

Value

dataframe without the CpGs that meet the conditions

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