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kunrzzz/
Monocyte_methylation

Name: Monocyte_methylation
Availability: InStock

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`.RData` File Structure

These files store CpG-level DNA methylation models together with the SNP sets and LD matrices used by each model.

Each .RData file contains exactly three objects:

CpG_mat is a data.frame with one row per CpG model in the file.

Columns:

SNPs is a named list. The list names are CpG IDs and match CpG_mat$CpG.

Each SNPs[[<CpG>]] entry is a data.frame containing the SNP model for that CpG, with columns:

Important storage note:

The weight column is stored as a one-column numeric matrix inside the data frame.
That embedded matrix has internal column name elastic_net.
Row names of each SNP table are SNP IDs.

MatrixLD is a named list. The list names are CpG IDs and match CpG_mat$CpG.

Each MatrixLD[[<CpG>]] entry is a square numeric matrix giving pairwise LD/correlation values for the SNPs used in the corresponding CpG model.

For a typical file:

nrow(CpG_mat) == length(SNPs) == length(MatrixLD).
CpG_mat$CpG, names(SNPs), and names(MatrixLD) align.
For a given CpG ID cg, SNPs[[cg]] contains the SNP model and MatrixLD[[cg]] contains the LD matrix for the same CpG model.
In most cases, nrow(SNPs[[cg]]) matches nrow(MatrixLD[[cg]]), and the SNP row names match the LD matrix row/column names.

load("chr1_87.RData")

str(CpG_mat)
names(SNPs)[1:3]

cg <- CpG_mat$CpG[1]
str(SNPs[[cg]])
dim(MatrixLD[[cg]])