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如何自己设定差异基因筛选标准 #4

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tu12dou opened this issue Oct 9, 2022 · 4 comments
Open

如何自己设定差异基因筛选标准 #4

tu12dou opened this issue Oct 9, 2022 · 4 comments
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enhancement New feature or request

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@tu12dou
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tu12dou commented Oct 9, 2022

这个包非常棒，如果能自己设定差异基因的p值及adj.p及FC就更好了
@xiayh17
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xiayh17 commented Oct 9, 2022

中文文档 https://www.yuque.com/xiayonghe/rnaseqstat2/preview_degcontainer
中有一例为更改pvalue的阈值
其他参数同理

@jnhv
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jnhv commented Sep 26, 2024

请问如何设置pvalue为阈值？我只找到了cutFDR ，cotFC的用法，似乎不能设置pvalue或qvalue为阈值？期待你的回复。

中文文档 https://www.yuque.com/xiayonghe/rnaseqstat2/preview_degcontainer 中有一例为更改pvalue的阈值 其他参数同理

@jnhv
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jnhv commented Sep 27, 2024

cutFDR，调整的似乎是pValue，而不是FDR或者adj.Pvalue?

@xiayh17
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xiayh17 commented Sep 28, 2024

是的，这两个函数是用于检测分组的数据所在列的，你可以修改之后重新编译一下

https://github.com/xiayh17/RNAseqStat2/blob/4ae8e3a7a3062c3be0ecfea7811320c7f17bfc17/R/utils.R#L32C1-L32C17

RNAseqStat2/R/utils.R

Line 32 in 4ae8e3a

pvalue_Identify <- function(res) {

@xiayh17 xiayh17 added the enhancement New feature or request label Sep 28, 2024
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@xiayh17 @jnhv @tu12dou