readtuples_output: read_tuples() output.

In markrobinsonuzh/DAMEfinder: Finds DAMEs - Differential Allelicly MEthylated regions

read_tuples() output.

Description

3 Patients from a previous study (Parker et al, 2018.) with colorectal cancer were sequenced and the normal and cancerous tissue of each patient was obtained. The data includes a subset of chromosome 19. Here one normal sample is not included.

Usage

readtuples_output

Format

A large list with 5 elements. Each element is a tibble with the coordinates of the pairs of CpG sites (tuples). Rest of the tibble contains:

MM

Number of reads with both CpG sites methylated

MU

Number of reads with first CpG site methylated

UM

Number of reads with second CpG site methylated

UU

Number of reads with both CpG sites unmethylated

cov

Coverage, total reads at tuple

inter_dist

Distance in bp between CpG sites

For further details, see https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6949/ sample names in in ArrayExpress do not necessarily match names given here!

markrobinsonuzh/DAMEfinder documentation built on April 7, 2023, 6:37 a.m.