Difference between revisions of "SNP matching (analysis)"
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;Analysis title | ;Analysis title | ||
| − | :SNP matching | + | :[[File:Mutations-SNP-matching-icon.png]] SNP matching |
;Provider | ;Provider | ||
:[[Institute of Systems Biology]] | :[[Institute of Systems Biology]] | ||
| + | ;Class | ||
| + | :{{Class|biouml.plugins.ensembl.analysis.SNPListToTrack}} | ||
| + | ;Plugin | ||
| + | :[[Biouml.plugins.ensembl (plugin)|biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)]] | ||
==== Description ==== | ==== Description ==== | ||
| − | Converts given list of SNPs to track and matches them to the genes. User should supply table where row identifiers are SNP names like <nowiki>'</nowiki>rs11111111<nowiki>'</nowiki> | + | Converts given list of SNPs to track and matches them to the genes. User should supply table where row identifiers are SNP names like <nowiki>'</nowiki>rs11111111<nowiki>'</nowiki>. |
==== Parameters: ==== | ==== Parameters: ==== | ||
* '''Table''' – Table of source genes | * '''Table''' – Table of source genes | ||
| − | * ''' | + | * '''Ensembl''' – Ensembl database version |
* '''5<nowiki>'</nowiki> region size''' – Include 5<nowiki>'</nowiki> region (promoter) of given size in bp | * '''5<nowiki>'</nowiki> region size''' – Include 5<nowiki>'</nowiki> region (promoter) of given size in bp | ||
* '''3<nowiki>'</nowiki> region size''' – Include 3<nowiki>'</nowiki> region of given size in bp | * '''3<nowiki>'</nowiki> region size''' – Include 3<nowiki>'</nowiki> region of given size in bp | ||
* '''Output non-matched''' – Whether to include in output table and track SNP<nowiki>'</nowiki>s which were not matched to any gene | * '''Output non-matched''' – Whether to include in output table and track SNP<nowiki>'</nowiki>s which were not matched to any gene | ||
* '''Column to copy''' – Name of additional column to be copied to created genes table | * '''Column to copy''' – Name of additional column to be copied to created genes table | ||
| + | * '''Ignore empty values''' – Ignore empty values during aggregator work | ||
* '''Aggregator''' – Operation to perform on column values if several SNP<nowiki>'</nowiki>s matched to single gene (<nowiki>'</nowiki>minimum<nowiki>'</nowiki>,<nowiki>'</nowiki>maximum<nowiki>'</nowiki>,<nowiki>'</nowiki>sum<nowiki>'</nowiki>,<nowiki>'</nowiki>average<nowiki>'</nowiki>) | * '''Aggregator''' – Operation to perform on column values if several SNP<nowiki>'</nowiki>s matched to single gene (<nowiki>'</nowiki>minimum<nowiki>'</nowiki>,<nowiki>'</nowiki>maximum<nowiki>'</nowiki>,<nowiki>'</nowiki>sum<nowiki>'</nowiki>,<nowiki>'</nowiki>average<nowiki>'</nowiki>) | ||
* '''Output track''' – Path to output track | * '''Output track''' – Path to output track | ||
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[[Category:Analyses]] | [[Category:Analyses]] | ||
| − | [[Category: | + | [[Category:Mutations (analyses group)]] |
[[Category:ISB analyses]] | [[Category:ISB analyses]] | ||
[[Category:Autogenerated pages]] | [[Category:Autogenerated pages]] | ||
Latest revision as of 18:15, 9 December 2020
- Analysis title
SNP matching
- Provider
- Institute of Systems Biology
- Class
SNPListToTrack- Plugin
- biouml.plugins.ensembl (Support for Ensembl database and Ensembl-specific analyses)
[edit] Description
Converts given list of SNPs to track and matches them to the genes. User should supply table where row identifiers are SNP names like 'rs11111111'.
[edit] Parameters:
- Table – Table of source genes
- Ensembl – Ensembl database version
- 5' region size – Include 5' region (promoter) of given size in bp
- 3' region size – Include 3' region of given size in bp
- Output non-matched – Whether to include in output table and track SNP's which were not matched to any gene
- Column to copy – Name of additional column to be copied to created genes table
- Ignore empty values – Ignore empty values during aggregator work
- Aggregator – Operation to perform on column values if several SNP's matched to single gene ('minimum','maximum','sum','average')
- Output track – Path to output track
- Output SNP table – Path to output table with additional annotation
- Output genes table – Path to output table containing all the genes matched to SNPs
