Output: predicted peaks

• 6424 genomic regions were found to have at least one sample with a peak (track hub, peaks_summary.tsv).
• 92135 peaks were detected overall, across 24 samples.
• Peak presence/absence matrices: (regions x samples), (regions x groups),
• Peak raw height matrix (regions x samples), mean coverage in peak, which is not comparable between samples, but is useful for plotting the segment mean on top of the raw coverage/count data,
• Peak normalized height matrix (regions x samples), log10(mean coverage in peak/mean coverage in background on the same sample), which is comparable between samples,
• Peak log-likelihood increase matrix (regions x samples) -- useful for ranking peaks (e.g. taking top 100 in each sample) -- wider and taller peaks are more likely, and have larger values in this matrix -- technically the values are computed as: nll_1 - nll_3, where nll_k is the negative log likelihood of the model with k segments (nll_1 is the model with one segment, no peak; nll_3 is the model with a peak, three segments, one change up and one change down).

Input: labeled genomic windows

	chunk	img
1	chr5:9779298-10259543
2	chr6:10642493-10706095
3	chr6:66860673-67897775
4	chr7:66775734-67059840
5	chr8:65927408-67266271
6	chr8:73348002-74081099
7	chr8:95917325-97000000
8	chr8:97000001-97495132

Input: genomic segmentation problems

Output: predicted group-specific peaks

These are great candidates for re-labeling.

aorta

168 genomic regions were predicted to have a common peak in the aorta group, and no peaks in other groups.

0 genomic regions were predicted to have no peaks in the aorta group, with a peak in all other groups.

aorta_Input

1 genomic region was predicted to have a common peak in the aorta_Input group, and no peaks in other groups.

14 genomic regions were predicted to have no peaks in the aorta_Input group, with a peak in all other groups.

colon

5 genomic regions were predicted to have a common peak in the colon group, and no peaks in other groups.

0 genomic regions were predicted to have no peaks in the colon group, with a peak in all other groups.

colon_Input

21 genomic regions were predicted to have a common peak in the colon_Input group, and no peaks in other groups.

41 genomic regions were predicted to have no peaks in the colon_Input group, with a peak in all other groups.

skeletalMuscle

332 genomic regions were predicted to have a common peak in the skeletalMuscle group, and no peaks in other groups.

16 genomic regions were predicted to have no peaks in the skeletalMuscle group, with a peak in all other groups.

skeletalMuscle_Input

0 genomic regions were predicted to have a common peak in the skeletalMuscle_Input group, and no peaks in other groups.

100 genomic regions were predicted to have no peaks in the skeletalMuscle_Input group, with a peak in all other groups.

thyroid

129 genomic regions were predicted to have a common peak in the thyroid group, and no peaks in other groups.