CpGsInfoAllRegions: Test associations of individual CpGs in multiple genomic...

In lissettegomez/coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

Description

Test associations of individual CpGs in multiple genomic regions with a continuous phenotype

Usage

CpGsInfoAllRegions(
  AllRegionNames_char,
  betas_df,
  pheno_df,
  contPheno_char,
  covariates_char,
  arrayType = c("450k", "EPIC")
)

Arguments

AllRegionNames_char	vector of character strings with location info for all the genomic regions. Each region should be specified in this format: "chrxx:xxxxxx-xxxxxx"
betas_df	data frame of beta values for all genomic regions, with row names = CpG IDs, column names = sample IDs
pheno_df	a data frame with phenotype and covariate variables, with variable "Sample" for sample IDs.
contPheno_char	character string of the continuous phenotype, to be tested against methylation values
covariates_char	character vector of covariate variables names
arrayType	Type of array, can be "450k" or "EPIC"

Value

a data frame with locations of the genomic region (Region), CpG ID (cpg), chromosome (chr), position (pos), and results for testing association of methylation in individual CpGs with continuous phenotype (slopeEstimate, slopePval), UCSC_RefGene_Name, UCSC_RefGene_Accession, UCSC_RefGene_Group

Examples

   data(betasChr22_df)
   data(pheno_df)
   AllRegionNames_char <- c("chr22:18267969-18268249", "chr22:18531243-18531447")

   CpGsInfoAllRegions(
     AllRegionNames_char,
     betas_df = betasChr22_df,
     pheno_df, contPheno_char = "stage",
     covariates_char = c("age.brain", "sex")
   )

lissettegomez/coMethDMR documentation built on April 25, 2021, 1:10 p.m.