This folder contains summary of 645 WGBS samples
Data is organizeed as matrices in 'csv' (comma separated) format per chromosome.
24 matrices for the x-coverage in 
./cov 
and in methylation folder for 3 different coverage thresholds( >=3, >=5, >=10):
./meth3
./meth5
./meth10

GemBS output (*cpg.bed file) that reports methylation values for C on (+) and (-) strands (in the CpG context) was psotprocessed:
CpG coverage was calculated as a sum of GemBS reported coverage of C and G (when available for both strands) and used as is, if reported for just one strand.
The methylation for the CpG is calculated as average for both strands weighted by the coverage. 

The number of rows (CpGs) per chromosome is (excluding the header row):
chr1    2375159
chr10   1388978
chr11   1333114
chr12   1315968
chr13   842469
chr14   862428
chr15   906026
chr16   1150891
chr17   1248328
chr18   756014
chr19   1056665
chr2    2192670
chr20   773477
chr21   428846
chr22   600892
chr3    1673293
chr4    1503429
chr5    1523709
chr6    1511189
chr7    1622825
chr8    1338200
chr9    1255728
chrX    1322709
chrY    169449

Coverage and methylation matrices have the number of rows corresponding to the number of CpGs on the corresponding chromosome. 
All methylation values for the CpGs for for which coverage is below the threshold are assigned -1.0 (missing value).

The first row is header containing EpiRR id (IHECRE) 
The first column contains the genomic location of C in the CpG
Matrices are sorted numerically on the CpG location.

18/10/2023
Misha Bilenky
mbilenky@bcgsc.ca