This object contains methylation levels (0 to 1) for cytosines in chromosome 1 that were covered by the DNA methylation microarray (Illumina 450k microarray). Each row corresponds to one cytosine and the coordinates for these cytosines are in the object brcaMCoord1, (data("brcaMCoord1"), hg38 genome). Only cytosines on chr1 are included to keep the example data small. Columns are patients, with TCGA patient identifiers as column names. The patients were selected based on their PC1 score from the PCA of DNA methylation on all chromosomes. The patients with the two highest PC1 scores and the two lowest PC1 scores are included (see data("brcaPCScores") for the actual scores). DNA methlyation data is Illumina 450k microarray data from breast cancer patients from The Cancer Genome Atlas (TCGA-BRCA, https://portal.gdc.cancer.gov/).
A matrix object
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