How to remove certain type of sample from a dataset?

[Edie Lee]

  I want to remove samples with EGFR aberration and without KRAS mutation, and only keep samples with no EGFR aberration and KRAS mutated lung adenocarcinoma. How can this be done?  

[Mary Goldman]

Hi Edie,

The easiest way to do this is to sequentially remove samples with EGFR aberrations and then keep samples with KRAS mutations.

First, start with Basic Tutorial 2 Part B (https://ucsc-xena.gitbook.io/project/tutorials/basic-tutorial-section-2#part-b) with the search term '(mis OR inframe) OR B:>0.5' to find samples with EGFR aberrations. Now, instead of creating subgroups, choose the option 'Remove samples'. This will remove samples that have an EGFR aberration. 

Next add a column with KRAS mutations (click on the add column to start, see Basic Tutorial 3 Part B (https://ucsc-xena.gitbook.io/project/tutorials/basic-tutorial-section-3) for an example of how to add a column). 

Erase the current search term. Now we need to search for mutations in KRAS (column E for me). While we could add each type of mutation separately, a trick is to search for the gene name itself for that column. This will select all samples that have a mutation in that column, regardless of what the mutation is. The search term ends up being 'E:KRAS'. 

Finally, choose 'Keep samples' to only keep those samples with a KRAS mutation.

Your final screen should be this: https://xenabrowser.net/?bookmark=aa3c8934170a88da30a3ccd6131c92be

More information about our supported search terms can be found here: https://ucsc-xena.gitbook.io/project/overview-of-features/filter-and-subgrouping/supported-search-terms-for-finding-samples, including information on searching mutation columns.

Please let me know if you have questions.

Best,

Mary

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Mary Goldman (she/her), Design and Outreach Engineer 

UCSC Xena

UC Santa Cruz Genomics Institute

Revealing life's code

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