The Progenetix resource provides pre-computed CNV frequencies for all its “collations” such as
This data can be accessed through the Progenetix API in data and image format.
Interval frequencies are per default stored in a 1Mb binned format. More information about the API use can be found in the IntervalFrequencies API documentation.
Typical cases for the use of collation-specific frequency data could be e.g. the visualization of CNV tracks with 3rd party tools such as Circos or integration in data analysis workflows, e.g. for comparing target genes to local, disease-specific CNV frequencies.
All cancer codes for a given classification system can be retrieved though:
For any of those codes one can create a
.pgxseg file downloader link for the
For the generation of CNV frequency plots, the same procedure as above for identifying existing frequency maps can be applied. CNV hsitograms in SVG format can be generated for download or embedding through a canonical service URL with added (single) collation code.
Plot parameters can be added to the request using a standard
syntax. Please be aware of the