Preprocessing

Removal of SNP-enriched Sites

SNP-based filtering was not performed because the site annotation does not include SNP information.

Removal of High Coverage Outlier Sites

389 sites was detected as a high coverage outlier in at least one sample and removed at this step. An outlier site is defined as one whose coverage exceeds 50 times the 0.95-quantile of coverage values in its sample. The list of removed sites is available in a dedicated table accompanying this report.

Masking of Sites with Low Coverage

A total of 56577949 sites with coverage less than 5 were masked by NA in the methylation table The numbers of masked sites per sample are available in a dedicated table accompanying this report.

Removal of Sites on Sex Chromosomes

62838 sites on sex chromosomes were removed at this step. The list of removed sites is available in a dedicated table accompanying this report.

Removal of Sites with (Many) Missing Values

1416417 sites were removed because they contain more than 108 missing values in the methylation table. This threshold corresponds to 50% of all samples. The total number of missing values in the methylation table before this filtering step was 316975222. A dedicated table of all removed sites is attached to this report.

The figure below shows the distribution of missing values per site.

Figure 1

Open PDF Figure 1

Histogram of number of sites that contain missing values. The vertical line, if visible, denotes the applied threshold.

Filtering Summary

As a final outcome of the filtering procedures, 1479255 sites and 0 samples were removed. These statistics are presented in a dedicated table that accompanies this report and visualized in the figure below.

Figure 2

Open PDF Figure 2

Fractions of removed values in the dataset after applying filtering procedures.

The figure below compares the distributions of the removed methylation β values and of the retained ones.

Plot type

Figure 3

Open PDF Figure 3

Comparison of removed and retained β values.Both distributions are estimated by randomly sampling 500000 values in each group.