mmcmcBayes (version 0.1.0)

compare_dmrs: Compare Differentially Methylated Regions (DMRs) from Two Methods

Description

Identifies and analyzes overlapping regions between two sets of differentially methylated regions (DMRs) detected by different methods. Computes overlap percentages to assess consistency between detection approaches.

Usage

compare_dmrs(rst1, rst2)

Value

A data frame with the following columns:

Chromosome

Chromosome name of the overlapping region

Start_CpG_Method1

Start CpG site from the first method

End_CpG_Method1

End CpG site from the first method

Start_CpG_Method2

Start CpG site from the second method

End_CpG_Method2

End CpG site from the second method

Overlap_Percentage

Percentage of overlap

Returns NULL if no overlaps are found.

Arguments

rst1

A data frame containing the first set of DMR results. Must contain columns: `Chromosome`, `Start_CpG`, and `End_CpG`.

rst2

A data frame containing the second set of DMR results. Must contain columns: `Chromosome`, `Start_CpG`, and `End_CpG`.

Author

Zhexuan Yang, Duchwan Ryu, and Feng Luan

Details

This function performs comparison of genomic regions between two DMR detection results. It identifies both partial and complete overlaps between regions and calculates overlap percentage by total region size.

See Also

Related functions in this package: mmcmcBayes for DMR detection using multi-stage MCMC, asgn_func for parameter estimation with ASGN distribution

Examples

# \donttest{
# Create sample DMR results
dmr_method1 <- data.frame(
  Chromosome = c("chr1", "chr1", "chr2"),
  Start_CpG = c("cg0001", "cg0050", "cg0100"),
  End_CpG = c("cg0020", "cg0070", "cg0150")
)

dmr_method2 <- data.frame(
  Chromosome = c("chr1", "chr2", "chr2"),
  Start_CpG = c("cg0005", "cg0120", "cg0090"),
  End_CpG = c("cg0025", "cg0160", "cg0110")
)

# Compare overlapping regions
overlaps <- compare_dmrs(dmr_method1, dmr_method2)
# }