#`[.default`(prefix_ad, attempts) 中的错误：无效的下标类型 'S4'

Question

我正在尝试运行此代码#甲基化数据：

prefix_ad <- data.frame(
Chromosome = c("Ecoli_K12", "Ecoli_K12", "Ecoli_K12", "Ecoli_K12", "Ecoli_K12", "Ecoli_K12", "Ecoli_K12", "Ecoli_K12", "Ecoli_K12", "Ecoli_K12"),
start = c(91, 153, 244, 249, 257, 259, 284, 298, 312, 1645),
end = c(91, 153, 244, 249, 257, 259, 284, 298, 312, 1645),
count = c(10, 20, 0, 11, 1, 15, 2, 5, 9, 8)
)

# Gene annotations
annotation <- data.frame(
Chromosome = c("Ecoli_K12", "Ecoli_K12", "Ecoli_K12"),
start = c(50, 210, 400),
end = c(200, 350, 600),
gene = c("gene_1", "gene_2", "gene_3")
 )

library(GenomicRanges)
library(dplyr)

# Create GRanges objects for methylation data and gene annotations
gr_methylation <- GRanges(
seqnames = prefix_ad$Chromosome,
ranges = IRanges(start = prefix_ad$start, end = prefix_ad$end)
 )

gr_genes <- GRanges(
seqnames = annotation$Chromosome,
ranges = IRanges(start = annotation$start, end = annotation$end),
id = annotation$gene)

# Match CpG sites to genes
hits <- findOverlaps(gr_methylation, gr_genes)

# Extract the overlapping data
methylation_within_genes <- prefix_ad[hits]

methylated_counts <- tapply(methylation_within_genes$count, methylation_within_genes$, sum, na.rm = TRUE)

我想要这样的输出：

chromosome  gene start    end methylated_count
  
Ecoli_K12 gene_1    50    200               30
Ecoli_K12 gene_2   210    350               34

我有两个问题：

1. 我做的事情正确吗？或者我需要使用任何替代解决方案吗？
2. 导致此错误的原因是什么？

methylation_within_genes <- prefix_ad[hits]

[.default

（prefix_ad，hits）中的错误：无效的下标类型“S4”

Answer 1

您的

hits

对象不能直接用于子集化操作，这里是子集

prefix_ad

。这就是错误告诉您的内容（诚然，以一种最无益的方式）。

hits

包含两个输入之间重叠的信息，称为

from

和

to

。当您将

hits

打印到控制台时，您会看到这一点。您可以使用

from()

和

to()

访问值，然后使用输出进行子集化，例如：

prefix_ad[from(hits),]
prefix_ad[to(hits),]