usage: pycoMeth Comp_Report [-h] -i METHCOMP_FN -g GFF3_FN -f REF_FASTA_FN
[-o OUTDIR] [-n N_TOP] [-d MAX_TSS_DISTANCE]
[--pvalue_threshold PVALUE_THRESHOLD]
[--min_diff_llr MIN_DIFF_LLR]
[--n_len_bin N_LEN_BIN] [--export_static_plots]
[--report_non_significant] [-v] [-q] [-p]
Generate an HTML report of significantly differentially methylated CpG
intervals from `Meth_Comp` text output. Significant intervals are annotated
with their closest transcript TSS.
optional arguments:
-h, --help show this help message and exit
Input/Output options:
-i METHCOMP_FN, --methcomp_fn METHCOMP_FN
Input tsv file generated by Meth_comp (can be
gzipped). At the moment only data binned by intervals
with Interval_Aggregate are supported. (required)
[str]
-g GFF3_FN, --gff3_fn GFF3_FN
Path to an **ensembl GFF3** file containing genomic
annotations. Only the transcripts details are
extracted. (required) [str]
-f REF_FASTA_FN, --ref_fasta_fn REF_FASTA_FN
Reference file used for alignment in Fasta format
(ideally already indexed with samtools faidx)
(required) [str]
-o OUTDIR, --outdir OUTDIR
Directory where to output HTML reports, By default
current directory (default: ./) [str]
Misc options:
-n N_TOP, --n_top N_TOP
Number of top interval candidates for which to
generate an interval report. If there are not enough
significant candidates this is automatically scaled
down. (default: 100) [int]
-d MAX_TSS_DISTANCE, --max_tss_distance MAX_TSS_DISTANCE
Maximal distance to transcription stat site to find
transcripts close to interval candidates (default:
100000) [int]
--pvalue_threshold PVALUE_THRESHOLD
pValue cutoff for top interval candidates (default:
0.01) [float]
--min_diff_llr MIN_DIFF_LLR
Minimal llr boundary for negative and positive median
llr. 1 is recommanded for vizualization purposes.
(default: 1) [float]
--n_len_bin N_LEN_BIN
Number of genomic intervals for the longest chromosome
of the ideogram figure (default: 500) [int]
--export_static_plots
Export all the plots from the reports in SVG format.
(default: False) [None]
--report_non_significant
Report all valid CpG islands, significant or not in
the text report. This option also adds a non-
significant track to the TSS_distance plot (default:
False) [None]
Verbosity options:
-v, --verbose Increase verbosity
-q, --quiet Reduce verbosity
-p, --progress Display a progress bar
(pycoMeth)