| methylation {pcev} | R Documentation |
Methylation values around BLK gene
Description
A dataset containing methylation values for cell-separated samples. The methylation was measured using bisulfite sequencing. The data also contains the genomic position of these CpG sites, as well as a binary phenotype (i.e. whether the sample comes from a B cell).
Usage
methylation
pheno
position
index
pheno2
position2
methylation2
Format
The data comes in four objects:
- methylation
Matrix of methylation values at 5,986 sites measured on 40 samples
- pheno
Vector of phenotype, indicating whether the sample comes from a B cell
- position
Data frame recording the position of each CpG site along the chromosome
- index
Index vector used in the computation of PCEV-block
- methylation2
Matrix of methylation values at 1000 sites measured on 40 samples
- pheno2
Vector of phenotype, indicating the cell type of the sample (B cell, T cell, or Monocyte)
- position2
Data frame recording the position of each CpG site along the chromosome
Details
Methylation was first measured at 24,068 sites, on 40 samples. Filtering was performed to keep the 25% most variable sites. See the vignette for more detail.
A second sample of the methylation dataset was extracted. This second dataset contains methylation values at 1000 CpG dinucleotides.
Source
Tomi Pastinen, McGill University, Genome Quebec.