如何在R中包含left_join循环?

Question

我有几个具有丰富的特定特性(OTU ID)的数据帧。例如，table1:

A tibble: 6 x 46
`OTU ID` V1.1.K1 V1.1.K2 V1.1.K3 V1.1.N1 V1.1.N2 V1.14.K16 V1.14.K17 V1.14.K18 V1.14.N0 V1.14.W16 V1.14.W17
<chr>      <dbl>   <dbl>   <dbl>   <dbl>   <dbl>     <dbl>     <dbl>     <dbl>    <dbl>     <dbl>     <dbl>
1 107273e~    2239    2861    1404   10255     585      4448      8340      5027      934       241      4983
2 bf83e8b~     174      95     406    4054     408     23383      6820     31184     2046       411       645
3 b744eae~      49      35     126    3440     245        83       443        18    11205       121       388
4 0e40fa4~      86      38     165    1015     111     10022      9973       228       90       638      2671
5 33ee4bb~      50      50      53      68      34       665       278      4816      218        38       136
6 c1c17b3~    2366    7838    7827     471      60       160        27        37      190        12       303
# ... with 34 more variables: V1.14.W18 <dbl>, V1.2.K4 <dbl>, V1.2.K5 <dbl>, V1.2.K6 <dbl>, V1.2.W4 <dbl>,
#   V1.2.W5 <dbl>, V1.2.W6 <dbl>, V1.21.K19 <dbl>, V1.21.K20 <dbl>, V1.21.K21 <dbl>, V1.21.N0 <dbl>,
#   V1.21.W19 <dbl>, V1.21.W20 <dbl>, V1.21.W21 <dbl>, V1.3.K7 <dbl>, V1.3.K8 <dbl>, V1.3.K9 <dbl>,
#   V1.3.W7 <dbl>, V1.3.W8 <dbl>, V1.3.W9 <dbl>, V1.4.K10 <dbl>, V1.4.K11 <dbl>, V1.4.K12 <dbl>, V1.4.W10 <dbl>,
#   V1.4.W11 <dbl>, V1.4.W12 <dbl>, V1.7.K13 <dbl>, V1.7.K14 <dbl>, V1.7.K15 <dbl>, V1.7.N0 <dbl>,
#   V1.7.W13 <dbl>, V1.7.W14 <dbl>, V1.7.W15 <dbl>, sum <dbl>

其他表看起来相似，只是丰度不同。然后我有一个分类法数据框架，其中包含有关特性的信息(OTU ID)。它被称为分类法，看起来像这样:

`OTU ID`                 Taxon                                                                       Confidence
<chr>                    <chr>                                                                            <dbl>
1 00009522ba8d1badfe92207~ d__Bacteria; p__Desulfobacterota; c__Desulfovibrionia; o__Desulfovibrional~      0.966
2 0000fb10633e8ad10a0f0b7~ d__Bacteria; p__Actinobacteriota; c__Actinobacteria; o__Micrococcales; f__~      0.999
3 0001d123420b59585627edf~ d__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f_~      1.00 
4 0001f7b8d2a9d04fbd0df3e~ d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Cytophagales; f__Bernarde~      1.00 
5 00026915bdc887a8587e62e~ d__Bacteria; p__Planctomycetota; c__Pla4_lineage; o__Pla4_lineage; f__Pla4~      0.997
6 0004a49903f29d739411b1c~ d__Archaea; p__Nanoarchaeota; c__Nanoarchaeia; o__Woesearchaeales; f__GW20~      0.777

由于OTU ID -列，丰度表应该与分类法表合并。对于一个数据帧，它使用以下代码:

table1_tax <- left_join(table1, taxonomy, by = "OTU ID")

现在我想把命令包含在for循环中，循环遍历我所有的丰度表，每个变量都应该与分类法文件结合起来，并分配给我可以使用的新变量。我不擅长for循环，所以请原谅我的错误。

#' get the tables in a list
tables <- mget(ls()[1:9])
#' as left_join can not loop over a list, I just extracted the names of the abundance tables in the variable. Was this step correct?
tables <- names(tables)
#' For Loop
for(i in 1:length(tables)) {
assign(paste0("tax_", tables[i]), left_join(tables[i], taxonomy, by= setnames("OTU ID")))
}

我得到的错误是:

Error in UseMethod("left_join") : 
no applicable method for 'left_join' applied to an object of class "character"

我该如何解决这个问题?你知道吗?谢谢你:)凯瑟琳

Answer 1

您是否得到了您想要的?

library(tidyverse)
# fake tables
df1 <- tribble(
~OTUID, ~V1, ~V2, ~V3, ~V4,
"09522ba", 2239, 2861, 1404, 10255,
"0fb1063", 174, 95, 406, 4054,
"b744eae", 49, 35, 126, 3440
)
df2 <- df3 <- df4 <- df1
# named list of tables
lst_tables <- list(df1 = df1, df2 = df2, df3 = df3, df4 = df4)
# fake taxonomy
taxo <-
tribble(
~OTUID, ~Taxon, ~Confidence,
"09522ba", "d__Bacteria p__Desulfobacterota c__Desulfovibrionia", 0.966,
"0fb1063", "d__Bacteria p__Actinobacteriota c__Actinobacteria", 0.999,
"1d12342", "d__Bacteria p__Proteobacteria c__Alphaproteobacteria", 1.00,
)
# 1) if you really want the loop
outbis <- list()
for(i in seq_along(lst_tables)) {
outbis[[i]] <- left_join(lst_tables[[i]], taxo, by = "OTUID")
names(outbis)[i] <- paste0("tax_", names(lst_tables)[i])
}
# 2) without the loop
out <-
map(lst_tables, ~ left_join(.x, taxo))