我有一些生物(微生物组)数据,其中我有一堆OTU,其单个名称在属和门级别之间的分类学分辨率不同。我试图得到一个比我给出的名字更低级别的分类表。
testnames <- c("Prevotella", "Bacteroides", "Enterobacteriaceae")
我发现taxize是一个有用的包,用于提取我正在寻找的信息。
library("taxize")
reclass <- classification(testnames, db = 'ncbi')
这会得到一个数据框列表
可以这样输入R:
structure(list(Prevotella = structure(list(name = c("cellular organisms",
"Bacteria", "FCB group", "Bacteroidetes/Chlorobi group", "Bacteroidetes",
"Bacteroidia", "Bacteroidales", "Prevotellaceae", "Prevotella"
), rank = c("no rank", "superkingdom", "no rank", "no rank",
"phylum", "class", "order", "family", "genus"), id = c("131567",
"2", "1783270", "68336", "976", "200643", "171549", "171552",
"838")), .Names = c("name", "rank", "id"), row.names = c(NA,
-9L), class = "data.frame"), Bacteroides = structure(list(name = c("cellular organisms",
"Bacteria", "FCB group", "Bacteroidetes/Chlorobi group", "Bacteroidetes",
"Bacteroidia", "Bacteroidales", "Bacteroidaceae", "Bacteroides"
), rank = c("no rank", "superkingdom", "no rank", "no rank",
"phylum", "class", "order", "family", "genus"), id = c("131567",
"2", "1783270", "68336", "976", "200643", "171549", "815", "816"
)), .Names = c("name", "rank", "id"), row.names = c(NA, -9L), class = "data.frame"),
Enterobacteriaceae = structure(list(name = c("cellular organisms",
"Bacteria", "Proteobacteria", "Gammaproteobacteria", "Enterobacterales",
"Enterobacteriaceae"), rank = c("no rank", "superkingdom",
"phylum", "class", "order", "family"), id = c("131567", "2",
"1224", "1236", "91347", "543")), .Names = c("name", "rank",
"id"), row.names = c(NA, -6L), class = "data.frame")), .Names = c("Prevotella",
"Bacteroides", "Enterobacteriaceae"))
我真的很想把事情变成一个数据框,我可以将其导入phyloseq作为分类表。例如。看起来像这样的东西:
名称Phylum Class Order Family Genus
Prevotella Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella
Bacteroides Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides
Enterobacteriaceae Proteobacteria Gammaproteobacteria Enterobacterales Enterobacteriaceae
当然,实现此目的的一种方法是创建一个循环,该循环将转到列表的每个元素,找到被调用的变量,即phylum,然后将其放入新的数据框中。也就是说,我觉得应该有更快的方式来应用这样的转换,使用像plyr或dplyr这样的东西。
我已经看到了一些似乎很接近的事情:
Converting nested list to dataframe
Turn a list of lists with unnamed entries into a data frame or a tibble
但他们似乎假设一个人不想保存的数据较少,并且每个元素的数据帧大小均匀。有什么建议吗?
答案 0 :(得分:1)
使用dplyr
和tidyr
:
library(dplyr)
library(tidyr)
tibble(names = names(list), list) %>%
unnest() %>%
filter(rank %in% c("phylum","class","order","family","genus")) %>%
select(-id) %>%
spread(rank, name) %>%
select(name = names, phylum, class, order, family, genus)
# A tibble: 3 × 6
name phylum class order family genus
* <chr> <chr> <chr> <chr> <chr> <chr>
1 Bacteroides Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides
2 Enterobacteriaceae Proteobacteria Gammaproteobacteria Enterobacterales Enterobacteriaceae <NA>
3 Prevotella Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella
这是做什么的:
tibble