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r - 从多列而不是单列聚合数据

问题描述

我有一个巨大的基因表达数据集，200k 个变量（行）和 170 个 obs（列）。下面是前几行/列

    Gene    Transcript_ID   V1  V2  V3  V4  V5
1   ENSG00000000003.14  ENST00000612152.4   0   6   0   3   15
2   ENSG00000000003.14  ENST00000373020.8   4   0   5   0   0
3   ENSG00000000003.14  ENST00000614008.4   0   0   0   0   0
4   ENSG00000000003.14  ENST00000496771.5   0   3   0   0   7

我正在尝试将所有数据分组以按基因表达。我正在利用现有语法通过一些元数据（基因 ID）对单个数据列进行分组，并试图让它为所有 170 个 obs 运行。语法如下，应该是一个非常简单的修复。

transcript_grouped <-aggregate(res$V1, by=list(Category=res$Gene), FUN=sum)

V1 是列名或观察/数据列，Res 是整个数据集，gene 是我希望数据分组的类别。此语法适用于 V1，但我需要为所有列运行此语法。

我尝试为所有列名创建一个变量，甚至手动粘贴它们。

dataColumns<- dataColumns = c("V1","V2","V3","V4","V5","V6","V7","V8","V9","V10","V11","V12","V13","V14","V15","V16","V17","V18","V19","V20","V21","V22","V23","V24","V25","V26","V27","V28","V29","V30","V31","V32","V33","V34","V35","V36","V37","V38","V39","V40","V41","V42","V43","V44","V45","V46","V47","V48","V49","V50","V51","V52","V53","V54","V55","V56","V57","V58","V59","V60","V61","V62","V63","V64","V65","V66","V67","V68","V69","V70","V71","V72","V73","V74","V75","V76","V77","V78","V79","V80","V81","V82","V83","V84","V85","V86","V87","V88","V89","V90","V91","V92","V93","V94","V95","V96","V97","V98","V99","V100","V101","V102","V103","V104","V105","V106","V107","V108","V109","V110","V111","V112","V113","V114","V115","V116","V117","V118","V119","V120","V121","V122","V123","V124","V125","V126","V127","V128","V129","V130","V131","V132","V133","V134","V135","V136","V137","V138","V139","V140","V141","V142","V143","V144","V145","V146","V147","V148","V149","V150","V151","V152","V153","V154","V155","V156","V157","V158","V159","V160","V161","V162","V163","V164","V165","V166") 

trans_grouped <-aggregate(res$dataColumns, by=list(Category=res$Gene), FUN=sum)

aggregate.data.frame(as.data.frame(x), ...) 中的错误：没有要聚合的行

请问如何循环这个以包含所有列？

标签： raggregate

解决方案

这个解决方案怎么样dplyr：

library(dplyr)
df %>%
  group_by(Gene) %>%
  summarise(across(starts_with("V"), ~sum(.)))
# A tibble: 2 x 4
  Gene     V1    V2    V3
* <chr> <dbl> <dbl> <dbl>
1 A         4     4     7
2 B         6     4     3

测试数据：

df <- data.frame(
  Gene = c("A", "B", "A", "B"),
  V1 = c(1,2,3,4),
  V2 = c(2,2,2,2),
  V3 = c(4,2,3,1)
)

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