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saezlab / liana

LIANA: a LIgand-receptor ANalysis frAmework
https://saezlab.github.io/liana/
GNU General Public License v3.0
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some LR pairs were not present #100

Closed Smilenone closed 1 year ago

Smilenone commented 1 year ago

I noticed that some LR pairs were not present for some celltype-pairs, i.e. for CD4T-B, I found NECTIN2-TIGIT LR pairs were not present in the result. Does this pairs were removed for thier low expression frequency in the corresponding celltypes?

And what if I want to save these LR pairs for ploting?

dbdimitrov commented 1 year ago

Hi @Smilenone,

Indeed liana will filter interactions with expr_prop lower than 0.1 by default. If you want to keep them check the return_all parameter :)

Hope this helps.

Smilenone commented 1 year ago

Hi,

Thanks for your response, is the keep_all parameter  in liana_wrap() function? Where can I find detalied description of this parameter?

------------------ 原始邮件 ------------------ 发件人: "saezlab/liana" @.>; 发送时间: 2023年4月6日(星期四) 晚上8:27 @.>; 抄送: "Qunlun @.**@.>; 主题: Re: [saezlab/liana] some LR pairs were not present (Issue #100)

Hi @Smilenone,

Indeed liana will filter interactions with expr_prop lower than 0.1 by default. If you want to keep it check the keep_all parameter :)

Hope this helps.

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dbdimitrov commented 1 year ago

?liana_wrap would do it, yes :)