R 从列表中的 Biostrings 格式提取基因

Question

我有一个序列列表

class(myseq)
[1] "list"

列表的每个元素内部都以 Biostrings package 的格式存储多个元素。 在此示例中，列表 myseq 包含 6 个样本

names(myseq)
 [1] "Sample-01" "Sample-02" "Sample-03" "Sample-04" "Sample-05" "Sample-06"

并且每个样本的格式为 Biostrings package

class(myseq[["Sample-01"]])
[1] "AAStringSet"
attr(,"package")
[1] "Biostrings"

myseqs[["Sample-01"]]
AAStringSet object of length 143:
      width seq                                                                                                                      names               
  [1]   453 MISIIKRFLGKRQPRQSAEHHYEFLPAHLALAQKPPSPFARLTAITLSIGVLAVLLWAY...VFPAQVQLNKNNIVIDGQTVELTPGMSVVAEIKTDKRRVIDYLLSPIREYQAEALRER IMEHDJCA_00190
  [2]   701 MSNNEGLTLICIHFYLSIISGNREQFKENANLTKTNNYKEELKKIQKANKVRITTKHSQ...VITIAHRLSTVRDCNRIIVLHQGAIVEQGSHQQLLTHGKQYKQLWQLQQELKQEETTA IMEHDJCA_00191
  ...   ... ...
[142]   275 MTAITISDQEYRDFSRFLESQCGIVLGDSKQYLVRSRLSPLVTKFKLASLSDLLRDVVT...RNVLIYFSPDMKSKVLNQMANSLNPGGYLLLGASESLTGLTDRFEMVRCNPGIIYKLK IMEHDJCA_03929
[143]   172 MPLLDSFTVDHTRMHAPAVRVAKTMQTPKGDTITVFDLRFTAPNKDILSEKGIHTLEHL...ESQNKIPELNEYQCGTAAMHSLDEAKQIAQNILAVGISVNRNDELALPEAMLKELKVD IMEHDJCA_04048

所以我想使用 data.frame 提取每个样本的特定基因

head(df)
           qseqid   samples gene
1  IMEHDJCA_02683 Sample-01 pilB
2  DIBHEKPI_01114 Sample-02 pilB
3  LLMDBGDK_00899 Sample-03 pilB
4  EBMGLGMO_01529 Sample-04 pilB
5  ILCJGNBA_00973 Sample-05 pilB
6  JAGNDBFC_01143 Sample-06 pilB

使用带有 for 循环的 qseqid 列提取每个样本的基因

genes <- c()
for(i in 1:nrow(df)){
    sample <- df[i,2]
    qseq_id <- df[i,1]

    seq <- myseqs[[sample]]
    genes[[i]] <- Biostrings::AAStringSet(seq[qseq_id])
}

我的问题是基因变量是一个列表

[[1]]
AAStringSet object of length 1:
    width seq                                                                                                                        names               
[1]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFDEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL IMEHDJCA_02683

[[2]]
AAStringSet object of length 1:
    width seq                                                                                                                        names               
[1]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFDEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL DIBHEKPI_01114

[[3]]
AAStringSet object of length 1:
    width seq                                                                                                                        names               
[1]   561 MTNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEQLSAIFGLPC...YEVMPFDEQLAEAIVKGASVQSLEMLAQQKGMMTLKDSGLEKLKQGITSLEELQRVLYL LLMDBGDK_00899

[[4]]
AAStringSet object of length 1:
    width seq                                                                                                                        names               
[1]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFNEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL EBMGLGMO_01529

[[5]]
AAStringSet object of length 1:
    width seq                                                                                                                        names               
[1]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFNEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL ILCJGNBA_00973

[[6]]
AAStringSet object of length 1:
    width seq                                                                                                                        names               
[1]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFNEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL JAGNDBFC_01143

我只想要一个包含 6 个样本基因的 Biostrings object，例如：

genes
AAStringSet object of length 6:
    width seq                                                                                                                                                                                                                                                                                       names               
[1]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFDEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL IMEHDJCA_02683
[2]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFDEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL DIBHEKPI_01114
[3]   561 MTNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEQLSAIFGLPC...YEVMPFDEQLAEAIVKGASVQSLEMLAQQKGMMTLKDSGLEKLKQGITSLEELQRVLYL LLMDBGDK_00899
[4]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFNEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL EBMGLGMO_01529
[5]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFNEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL ILCJGNBA_00973
[6]   562 MQSNLATILRQANQLSLTQEQACRETIQASGVTAPEALLQLGFFQPDELTEKLSAIFGLP...YEVMPFNEQLAEAIVKGASVQSLEMLARQKGMMTLKDSGLEKLKQGITSLEELQRVLYL JAGNDBFC_01143

我试图在没有 [[i]] 的情况下存储基因变量：

genes <- Biostrings::AAStringSet(seq[qseq_id])

但它只保留最后一个序列。

如果我手动执行，将类似于：

S01 <- Biostrings::AAStringSet(myseqs[["Sample-01"]]["IMEHDJCA_02683"])
S02 <- Biostrings::AAStringSet(myseqs[["Sample-02"]]["DIBHEKPI_01114"])

以此类推 Sample-03 到 Sample-n.... 然后生成 Biostrings object

genes <- c(S01, S02, S03, S04, S05, S06) 

有没有人知道怎么做？？？

非常感谢 ！！！

Answer 1

您可以取消列出 AAStringSet object，例如

library(Biostrings)

a <- AAString("MISIIKRFLGKRQPRQSAEHHYEFLPAHLALAQKPPSPFARLTAITLSIGVLAVLLWAYVFPAQVQLNKNNIVIDGQTVELTPGMSVVAEIKTDKRRVIDYLLSPIREYQAEALRER")
b <- AAString("MTAITISDQEYRDFSRFLESQCGIVLGDSKQYLVRSRLSPLVTKFKLASLSDLLRDVVTRNVLIYFSPDMKSKVLNQMANSLNPGGYLLLGASESLTGLTDRFEMVRCNPGIIYKLK")
myseqs <- list("Sample-01" = AAStringSet(c("IMEHDJCA_02683" = a)),
               "Sample-02" = AAStringSet(c("DIBHEKPI_01114" = b)))
class(myseqs)
#> [1] "list"
names(myseqs)
#> [1] "Sample-01" "Sample-02"
myseqs[["Sample-01"]]
#> AAStringSet object of length 1:
#>     width seq                                               names               
#> [1]   117 MISIIKRFLGKRQPRQSAEHHYE...KRRVIDYLLSPIREYQAEALRER IMEHDJCA_02683

class(myseqs[["Sample-01"]])
#> [1] "AAStringSet"
#> attr(,"package")
#> [1] "Biostrings"

df <- read.table(text = "       qseqid   samples gene
1 IMEHDJCA_02683 Sample-01 pilB
2 DIBHEKPI_01114 Sample-02 pilB", header = TRUE)
df
#>           qseqid   samples gene
#> 1 IMEHDJCA_02683 Sample-01 pilB
#> 2 DIBHEKPI_01114 Sample-02 pilB

genes <- c()
for(i in 1:nrow(df)){
  sample <- df[i,2]
  qseq_id <- df[i,1]
  
  seq <- myseqs[[sample]]
  genes[[i]] <- unlist(AAStringSet(seq[qseq_id]))
}

genes_object <- AAStringSet(genes)

genes_object
#> AAStringSet object of length 2:
#>     width seq
#> [1]   117 MISIIKRFLGKRQPRQSAEHHYEFLPAHLALAQK...MSVVAEIKTDKRRVIDYLLSPIREYQAEALRER
#> [2]   117 MTAITISDQEYRDFSRFLESQCGIVLGDSKQYLV...GGYLLLGASESLTGLTDRFEMVRCNPGIIYKLK

^{由reprex package (v2.0.1) 于 2022 年 8 月 9 日创建}

但是，不幸的是，副作用是您丢失了@ranges@NAMES 属性（即“名称”列消失了）。

---

我认为您可以将名称添加到新的 object，但您需要检查它是否适用于您的用例（即检查结果是否正确）：

library(Biostrings)

a <- AAString("MISIIKRFLGKRQPRQSAEHHYEFLPAHLALAQKPPSPFARLTAITLSIGVLAVLLWAYVFPAQVQLNKNNIVIDGQTVELTPGMSVVAEIKTDKRRVIDYLLSPIREYQAEALRER")
b <- AAString("MTAITISDQEYRDFSRFLESQCGIVLGDSKQYLVRSRLSPLVTKFKLASLSDLLRDVVTRNVLIYFSPDMKSKVLNQMANSLNPGGYLLLGASESLTGLTDRFEMVRCNPGIIYKLK")
myseqs <- list("Sample-01" = AAStringSet(c("IMEHDJCA_02683" = a)),
               "Sample-02" = AAStringSet(c("DIBHEKPI_01114" = b)))
class(myseqs)
#> [1] "list"
names(myseqs)
#> [1] "Sample-01" "Sample-02"
myseqs[["Sample-01"]]
#> AAStringSet object of length 1:
#>     width seq                                               names               
#> [1]   117 MISIIKRFLGKRQPRQSAEHHYE...KRRVIDYLLSPIREYQAEALRER IMEHDJCA_02683

class(myseqs[["Sample-01"]])
#> [1] "AAStringSet"
#> attr(,"package")
#> [1] "Biostrings"

df <- read.table(text = "       qseqid   samples gene
1 IMEHDJCA_02683 Sample-01 pilB
2 DIBHEKPI_01114 Sample-02 pilB", header = TRUE)
df
#>           qseqid   samples gene
#> 1 IMEHDJCA_02683 Sample-01 pilB
#> 2 DIBHEKPI_01114 Sample-02 pilB

genes <- c()
qseqids <- c()
for(i in 1:nrow(df)){
  sample <- df[i,2]
  qseq_id <- df[i,1]
  
  seq <- myseqs[[sample]]
  genes[[i]] <- unlist(AAStringSet(seq[qseq_id]))
  qseqids <- c(qseqids, qseq_id)
}
names(genes) <- qseqids

genes_object <- AAStringSet(genes)
genes_object
#> AAStringSet object of length 2:
#>     width seq                                               names               
#> [1]   117 MISIIKRFLGKRQPRQSAEHHYE...KRRVIDYLLSPIREYQAEALRER IMEHDJCA_02683
#> [2]   117 MTAITISDQEYRDFSRFLESQCG...SLTGLTDRFEMVRCNPGIIYKLK DIBHEKPI_01114

^{由reprex package (v2.0.1) 于 2022 年 8 月 9 日创建}