Data format
Input:
CpG methylation matrix: methylation.mat
The first column should be the chromosome ID and the second column should be the position of the CpG. The following columns should be samples. Format: tab-separated, value range: 0-1, missing values representated by . (Please do NOT use . to represent zero!), and genomic position sorted.
If you have BED files and don’t know how to generate this matrix, click Example.
| chr | pos | sample_1 | sample_2 | sample_3 | … |
|---|---|---|---|---|---|
| chr1 | 100 | 0.1 | 0.2 | . | … |
| chr1 | 200 | 0.1 | 0.5 | 0.3 | … |
| chr2 | 100 | 1 | . | 0 | … |
| … | … | … | … | … | … |
Group information table: samples_groups.tsv
This table should have two columns: ID and Group. The sample IDs in this table should be exactly matched to the sample IDs in methylation.mat. Format: tab-separated.
| ID | Group |
|---|---|
| sample_1 | Group_A |
| sample_2 | Group_B1 |
| sample_3 | Group_B2 |
| … | … |
Output:
DMR table: /output_dir/DMRs.tsv
This table contains all DMRs found by metilene3. Format: tab-separated, working with iso-8859-1.
| Column name | Description |
|---|---|
| chr | chromosome ID. |
| start | start position of the DMR. |
| stop | stop position of the DMR. |
| q | Bonferroni adjusted p-values based on MWU-test p-values. |
| meandiff | (for developers) mean difference between the methylated group and the unmethylated group. |
| length | number of CpGs in the DMR. |
| mwu | MWU-test p-value. |
| p | 2D KS-test p-value. |
| mean | mean values for each sample/group - the order (ID) of groups can be found in /output_dir/groupID.tsv. |
| sig.comparison | (for developers) status of samples/groups: 1 for unmethylated, 2 for intermediate and 3 for methylated - the order (ID) of groups can be found in /output_dir/groupID.tsv. |
| meandiffabs | absolute mean difference between the methylated group and the unmethylated group. |
| #Hypo/Int/Hyper | number of hypomethylated/intermediate/hypermethylated (Hypo/Int/Hyper) samples/groups. |
| meanHypo/Int/Hyper | mean of hypomethylated/intermediate/hypermethylated (Hypo/Int/Hyper) samples/groups. |
| Hypo/Int/Hyper-samples/groups | the samples (unsupervised DMRs) or groups (supervised DMRs) that are classified as hypomethylated/intermediate/hypermethylated (Hypo/Int/Hyper). |
| distanceToTSS | distance to the transcription start site annotated by ChIPSeeker. (optional, only if the parameter annotation -anno is set.) |
| ENSEMBL | ENSEMBL ID annotated by ChIPSeeker. (optional, only if the parameter annotation -anno is set.) |
| SYMBOL | gene symbol annotated by ChIPSeeker. (optional, only if the parameter annotation -anno is set.) |
| anno | genomic annotation by ChIPSeeker. (optional, only if the parameter annotation -anno is set.) |
| DMTree | (for developers) DMRs that are associated with DMTree splits. |