Find Top5 min and max values per group in dataframe (determine min and max differentially expressed genes)

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英文:

Find Top5 min and max values per group in dataframe (determine min and max differentially expressed genes)

问题

In a dataframe of differential expression results, find the 5 genes per group that are maximally and minimally regulated (= highest and lowest log fold change).

example data

  1. set.seed(47)
  2. gene_creator <- paste("gene",1:100,sep="")
  3. genes = sample(gene_creator,8)
  5. dex_A <- data.frame(
  6.   gene = genes,
  7.   group = "group_A",
  8.   logFC = sample(c(-5:5), replace=T, size=8),
  9.   FDR = sample(c(0.01,1), replace=T, size=8)
  10. )
  12. dex_B <- data.frame(
  13.   gene = genes,
  14.   group = "group_B",
  15.   logFC = sample(c(-5:5), replace=T, size=8),
  16.   FDR = sample(c(0.01,1), replace=T, size=8)
  17. )
  19. dex_df <- rbind(dex_A, dex_B)

solution (not working)

  1. library(tidyverse)
  2. dex_df %>%
  3.   filter(FDR < 0.05) %>%
  4.   group_by(group) %>%
  5.   mutate(
  6.     top5 = slice_max(logFC, n = 5),
  7.     min5 = slice_min(logFC, n = 5))
英文:

In a dataframe of differential expression results, find the 5 genes per group that are maximally and minimally regulated (= highest and lowest log fold change).
My solution with mutate and slice_max/min somehow wont work.

example data

  1. set.seed(47)
  2. gene_creator <- paste("gene",1:100,sep="")
  3. genes = sample(gene_creator,8)
  5. dex_A <- data.frame(
  6.   gene = genes,
  7.   group = "group_A",
  8.   logFC = sample(c(-5:5), replace=T, size=8),
  9.   FDR = sample(c(0.01,1), replace=T, size=8)
  10. )
  12. dex_B <- data.frame(
  13.   gene = genes,
  14.   group = "group_B",
  15.   logFC = sample(c(-5:5), replace=T, size=8),
  16.   FDR = sample(c(0.01,1), replace=T, size=8)
  17. )
  19. dex_df <- rbind(dex_A, dex_B)

solution (not working)

  1. library(tidyverse)
  2. dex_df %>%
  3.   filter(FDR < 0.05) %>%
  4.   group_by(group) %>%
  5.   mutate(
  6.     top5 = slice_max(logFC, n = 5),
  7.     min5 = slice_min(logFC, n = 5))

答案1

得分: 3

You cannot use slice_max() or slice_min() directly with mutate. You have to use them separately and row bind them, i.e.

您不能直接在mutate中使用slice_max()或slice_min()。您必须将它们分开使用，然后将它们行绑定，即：

英文:

You cannot use slice_max() or slice_min() directly with mutate. You have to use them separately and row bind them, i.e.

  1. bind_rows(dex_df %>%
  2.             filter(FDR < 0.05) %>%
  3.             group_by(group) %>%
  4.             slice_max(logFC, n = 5) %>%
  5.             mutate(rank = "top5"),
  6.           dex_df %>%
  7.             filter(FDR < 0.05) %>%
  8.             group_by(group) %>%
  9.             slice_min(logFC, n = 5) %>%
  10.             mutate(rank = "min5"))

huangapple
  • 本文由 发表于 2023年4月17日 16:56:35
  • 转载请务必保留本文链接：https://go.coder-hub.com/76033360.html
  • dplyr
  • r
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