英文:
fisher exact using tidyr or dplyr approach
问题
我有一个包含两组数据的数据框，分别是肿瘤组和正常组。对于每个位点/行，我想要计算在肿瘤组和正常组之间使用Methyl和UnMethy的Fisher精确度。
我正在寻找如何将数据转换为使用dplyr方法计算每个位点的Fisher精确度。
methyl_dat <- data.frame(loci = c("site1", "site2", "site3", "site4"),
Methy.tumor = c(50, 5, 60, 12),
UnMethy.tumor = c(60, 0, 65, 5),
Methy.Normal = c(13, 5, 22, 3),
UnMethy.Normal = c(86, 0, 35, 3))
这里是Fisher精确度的计算策略
对于位点1
正常组
肿瘤组 Methyl UnMethy
Methy 50 13
UnMethy 60 86
英文:
I have data dataframe with two groups, Tumor and Normal. for each site/row i want calculate fischer exact for using Methyl UnMethy between Tumor and Normal
I'm looking for how to transform data to calculate fisher exact for each site using dplyr approach.
methyl_dat <- data.frame(loci = c("site1", "site2", "site3", "site4"),
Methy.tumor = c(50, 5, 60, 12),
UnMethy.tumor = c(60, 0, 65, 5),
Methy.Normal = c(13, 5, 22, 3),
UnMethy.Normal = c(86, 0, 35, 3) )
Here is Fischer exact strategy
for site 1
Normal
Tumor Methyl UnMethy
Methy 50 13
UnMethy 60 86
</details>
# 答案1
**得分**: 5
apply(methyl_dat[-1], 1, \(x)fisher.test(matrix(x,2)), simplify = F)
<details>
<summary>英文:</summary>
consider doing:
apply(methyl_dat[-1], 1, \(x)fisher.test(matrix(x,2)), simplify = F)
</details>
# 答案2
**得分**: 2
添加一个`dplyr`解决方案：
```r
library(dplyr, warn.conflicts = FALSE)
data.frame(loci = c("site1", "site2", "site3", "site4"),
Methy.tumor = c(50, 5, 60, 12),
UnMethy.tumor = c(60, 0, 65, 5),
Methy.Normal = c(13, 5, 22, 3),
UnMethy.Normal = c(86, 0, 35, 3) ) %>%
group_by(loci) %>%
summarise(
p_val = fisher.test(matrix(c_across(everything()), 2))$p.val
)
#> # A tibble: 4 × 2
#> loci p_val
#> <chr> <dbl>
#> 1 site1 0.000000392
#> 2 site2 1
#> 3 site3 0.263
#> 4 site4 0.621
创建于2023-06-01，使用reprex v2.0.2
英文:
Adding a dplyr solution:
library(dplyr, warn.conflicts = FALSE)
data.frame(loci = c("site1", "site2", "site3", "site4"),
Methy.tumor = c(50, 5, 60, 12),
UnMethy.tumor = c(60, 0, 65, 5),
Methy.Normal = c(13, 5, 22, 3),
UnMethy.Normal = c(86, 0, 35, 3) ) %>%
group_by(loci) %>%
summarise(
p_val = fisher.test(matrix(c_across(everything()), 2))$p.val
)
#> # A tibble: 4 × 2
#> loci p_val
#> <chr> <dbl>
#> 1 site1 0.000000392
#> 2 site2 1
#> 3 site3 0.263
#> 4 site4 0.621
<sup>Created on 2023-06-01 with reprex v2.0.2</sup>
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