Quickstart¶
Install PRISM with pip.
$ pip install subclone-prism
Run analysis.
------------------------------
Extract epiloci from BAM file.
------------------------------
$ prism extract -i sample.bam -o sample.met
-------------------------------------------------------------------
Preprocess epiloci to get finer estimates of epigenetic subclones
and to rescue more fingerprint epiloci from noisy methylation data.
-------------------------------------------------------------------
$ prism preprocess -i sample.met -o sample.corrected.met
----------------------------------------------
Infer the subclonal composition of the sample.
----------------------------------------------
If you want 1-sample deconvolution, run:
$ prism deconvolute -i sample.corrected.met -o sample.prism.result
or if you want 2-sample deconvolution, run:
$ prism deconvolute -i sample1.corrected.met sample2.corrected.met -o sample.prism.result
--------------------------------------------
Scatterplot for visualization of the result.
--------------------------------------------
$ prism scatter -i sample.prism.result -o sample.png
--------------------------------------------------------------------
Annotation of fingerprint epiloci for functional characterization of
discovered epigenetic subclones.
--------------------------------------------------------------------
$ prism annotate -i sample.prism.result -o sample.prism.annotated.result \
--beds annotation_a.bed annotation_b.bed \
--annotation-names ANNOTATION-A ANNOTATION-B
The PRISM analysis is done in three steps: extract - preprocess - deconvolute.