Use Case - Download or Plot CNV Frequencies

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.

Example CNV histogram with custom parameters

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.


Contents


Example Procedure - Download CNV Frequencies

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.

Getting cancer type CNV frequencies

All cancer codes for a given classification system can be retrieved though:

Download the data file

For any of those codes one can create a .pgxseg file downloader link for the “IntervalFrequencies” service:

Examples

Example Procedure - Download or embed CNV frequency plot

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.

Examples

Additional plot parameters

Plot parameters can be added to the request using a standard &-__parameter__=__value__ syntax. Please be aware of the - prefix.

Links

@mbaudis 2021-05-14
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