僅保留具有匹配列名的列

Question

在按列合並之前，我想保留 SummarizedExperiment 數據類型的所有三個數據幀met.kirp.450 、 met.kirc.450和met.kich.450中的列名。

首先，我在提交具有這些匹配列的數據幀之前找到匹配列match.col 。 然后，我執行了SummarizedExperiment::cbind 。

dflist <- list(met.kirp.450, met.kirc.450, met.kich.450)
match.col <- Reduce(function(x, y){intersect(x, names(y))}, dflist, init = names(dflist[[1]]))
met.kirp.450 <- met.kirp.450[match.col,]
met.kirc.450 <- met.kirc.450[match.col,]
met.kich.450 <- met.kich.450[match.col,]

met.kipan <- SummarizedExperiment::cbind(met.kirp.450, met.kirc.450, met.kich.450)

追溯：

Error in .aggregate_and_align_all_colnames(all_colnames, strict.colnames = strict.colnames) : 
  the DFrame objects to combine must have the same column names

我無法打印 dput，因為即使是最小的dput(met.kirp.450[1,1])也太長了。

數據：

library(TCGAbiolinks)

query.met.kirp <- GDCquery(
  project = "TCGA-KIRP", 
  legacy = TRUE,
  data.category = "DNA methylation",
  platform = "Illumina Human Methylation 450", 
)
GDCdownload(query.met.kirp)

query.met.kirc <- GDCquery(
  project = "TCGA-KIRC", 
  legacy = TRUE,
  data.category = "DNA methylation",
  platform = "Illumina Human Methylation 450", 
)
GDCdownload(query.met.kirc)

query.met.kich <- GDCquery(
  project = "TCGA-KICH", 
  legacy = TRUE,
  data.category = "DNA methylation",
  platform = "Illumina Human Methylation 450", 
)
GDCdownload(query.met.kich)

met.kirp.450 <- GDCprepare(
  query = query.met.kirp,
  save = TRUE, 
  save.filename = "gbmDNAmet450k.rda",
  summarizedExperiment = TRUE
)

met.kirc.450 <- GDCprepare(
  query = query.met.kirc,
  save = TRUE, 
  save.filename = "gbmDNAmet450k.rda",
  summarizedExperiment = TRUE
)

met.kich.450 <- GDCprepare(
  query = query.met.kich,
  save = TRUE, 
  save.filename = "gbmDNAmet450k.rda",
  summarizedExperiment = TRUE
)

Answer 1

由於對象采用 SummarizedExperiment 格式，因此可以從y@colData@rownames檢索列名，其中colData表示列數據。

match.cols <- Reduce(function(x, y){intersect(x, y@colData@rownames)}, dflist, init = colnames(dflist[[1]]))

met.kirp.450.new <- met.kirp.450[,match.cols]
met.kirc.450.new <- met.kirc.450[,match.cols]
met.kich.450.new <- met.kich.450[,match.cols]

met.kipan <- SummarizedExperiment::cbind(met.kirp.450.new, met.kirc.450.new, met.kich.450.new)