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Performs the entire DMRichR analysis pipeline, which runs most functions in the package.

Usage

DM.R(
  genome = c("hg38", "hg19", "mm10", "mm9", "rheMac10", "rheMac8", "rn6", "danRer11",
    "galGal6", "bosTau9", "panTro6", "dm6", "susScr11", "canFam3", "TAIR10", "TAIR9"),
  coverage = 1,
  perGroup = 0.75,
  minCpGs = 5,
  maxPerms = 10,
  maxBlockPerms = 10,
  cutoff = 0.05,
  testCovariate = testCovariate,
  adjustCovariate = NULL,
  matchCovariate = NULL,
  cores = 20,
  GOfuncR = TRUE,
  sexCheck = FALSE,
  EnsDb = FALSE
)

Arguments

genome

Character specifying the genome.

coverage

Numeric specifying the CpG coverage cutoff (1x recommended).

perGroup

Numeric indicating percent of samples per a group to apply the CpG coverage cutoff to (from 0 to 1).

minCpGs

Numeric for minimum number of CpGs for a DMR.

maxPerms

Numeric indicating number of permutations for the DMR analysis.

maxBlockPerms

Numeric indicating number of permutations for the block analysis.

cutoff

Numeric indicating the cutoff value for the single CpG coefficient utilized to discover testable background regions. Values range from 0 to 1 and 0.05 (5 percent) is the default. If you get too many DMRs you should try 0.1 (10 percent).

testCovariate

Character indicating factor of interest from the design matrix. Only case vs control is supported.

adjustCovariate

Character vector indicating discrete and continuous variables to adjust for based on the design matrix. Multiple variables can be provided.

matchCovariate

Character indicating the variable in the design matrix to block for when constructing permutations. Only a single variable can be provided and it cannot also be an adjustCovariate.

cores

Numeric specifying the number of cores to use. 20 is recommended.

GOfuncR

Logical indicating whether to run a GOfuncR GO analysis.

sexCheck

Logical indicating whether to confirm sex of each sample. This is highly recommended if your analysis has males and females and will also drop the sex chromosomes. You should also include the sex variable as an adjustCovariate.

EnsDb

Logical indicating whether to to select Ensembl transcript annotation database. This is recommended for non-model organisms.

Details

DM.R