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.