Unsupervised mode
With unsupervised mode, each sample will be regarded as one group.
python /path_to_metilene3/metilene3.py [-i <string>] [-o <string>] [optional options...]
Parameters:
(Go to DMR calling and DMTree for more details!)
| parameter | unit | default | description |
|---|---|---|---|
| -i, --input | string | the input methylation data, format | |
| -o, --output | string | the output directory | |
| -t, --threads | integer | 1 | (optional) number of threads |
| -s, --seed | integer | 1 | (optional) set seed for random generator |
| -O, --outputImputed | bool | False | (optional) True or False, save the CpG methylation matrix with imputed values as file imputed.tsv |
| -p, --verbose | bool | False | (optional) True or False, track the process |
| -M, --maxdist | integer | 300 | (optional) maximum distance between two CpG, details |
| -m, --minCpGs | integer | 10 | (optional) minimum CpGs, details |
| -d, --minMethDiff | double | 0.1 | (optional) minimum mean methylation difference, details |
| -r, --minDMR | integer | 5 | (optional) minimum CpGs with minimum mean methylation difference in a segment, details |
| -v, --valley | double | 0.7 | (optional) a cutoff for the difference between global and regional methylation differences, details |
| -D, --minMethDiffHigh | double | 0.5 | (optional) minimum mean methylation difference for DMTree and GSEA, similar to -d, --minMethDiff but a higher value will be recommanded to reduce the number of false positive DMRs, details |
| -u, --clusteringRatio | double | 0.5 | (optional) maximum ratio of CpGs with minimum difference in a cluster, details |
| -n, --minNSamples | integer | 3 | (optional) minimum samples in a cluster, details |
| -w, --minSumDMRs | integer | 100 | (optional) minimum sum of DMR weights to split samples, details |
| -plot, --visualization | bool | False | (optional) plot PCA and heatmap based on DMR methylation |
| -anno, --annotation | string | (optional) hg19 or hg38, use ChIPseeker to annotate the DMRs | |
| -refs, --refSeq | string | (optional) reference genome, fasta file, for sequence annotation | |
| -gsea, --genesets | string | (optional) geneset gmt file for GSEA | |
| -wsup, --withSupervised | bool | True | (optional) run supervised mode after clustering |