methylation: Methylation values around BLK gene
In pcev: Principal Component of Explained Variance

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).

methylation

pheno

position

index

pheno2

position2

methylation2

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

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.

Tomi Pastinen, McGill University, Genome Quebec.

pcev documentation built on May 2, 2019, 12:45 p.m.