Doubt about splicing analysis

[RamonSLPS]

Hello, I am doing an alternative splicing analysis of immune-associated genes among 4 conditions (3 comparisons). I was able to get the general splicing comparative summary ("extractSplicingSummary" and "extractSplicingEnrichment"). So I would like to know if there is a way to retrieve a list of which specific genes these events were identified in (as I need to know how many of them are immune and what their functions are) and in which of the conditions. (Example: in condition 1, TLR7 had 3 exon skipping events; but in condition 2, the same gene had 5 exon skipping events)

Note: I imagine that the "SwitchList$AlternativeSplicingAnalysis" does not show this type of information, as it contaions the events that occurred in all conditions at the same time. Or am I reading it wrong?

Thanks in advance, Ramon Lopes.

[kvittingseerup]

Yes. Both functions can return the data instead of plotting it. Take a look at the documentation 😊

Cheers Kristoffer

tor. 22. jun. 2023 kl. 22.07 skrev Ramon Lopes @.***>:

Hello, I am doing an alternative splicing analysis of immune-associated genes among 4 conditions (3 comparisons). I was able to get the general splicing comparative summary ("extractSplicingSummary" and "extractSplicingEnrichment"). So I would like to know if there is a way to retrieve a list of which specific genes these events were identified in (as I need to know how many of them are immune and what their functions are) and in which of the conditions. (Example: in condition 1, TLR7 had 3 exon skipping events; but in condition 2, the same gene had 5 exon skipping events)

Note: I imagine that the "SwitchList$AlternativeSplicingAnalysis" does not show this type of information, as it contaions the events that occurred in all conditions at the same time. Or am I reading it wrong?

Thanks in advance, Ramon Lopes.

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-- Cheers Kristoffer

[RamonSLPS]

I confess that I didn't understand exactly the meaning of isoforms used less/more in the splicingsummary. Can you explain? Does it refers to condition 1 vs condition 2 (used less refers to 1 and more to 2)? if I do isoform used less + isoform used more for my condition = the total number of events of the same type?

How can I return the total number of splicing and types of each condition without comparisson? I have four conditions: heated_control, heated_infected, cold_control and cold_infected. How can I return the total numbers of alternative splicing events and which genes for each one condition?