Question

我正在尝试在R中订购一个变量，这是一个包含三个我想要订购的子串的文件名列表。文件名的格式如下：

MAF001.incMHC.zPGS.S1
MAF002.incMHC.zPGS.S1
MAF003.incMHC.zPGS.S1
MAF001.incMHC.zPGS.S2
MAF002.incMHC.zPGS.S2
MAF003.incMHC.zPGS.S2
MAF001.noMHC_incRS148.zPGS.S1
MAF002.noMHC_incRS148.zPGS.S1
MAF003.noMHC_incRS148.zPGS.S1
MAF001.noMHC_incRS148.zPGS.S2
MAF002.noMHC_incRS148.zPGS.S2
MAF003.noMHC_incRS148.zPGS.S2
MAF001.noMHC.zPGS.S1
MAF002.noMHC.zPGS.S1
MAF003.noMHC.zPGS.S1
MAF001.noMHC.zPGS.S2
MAF002.noMHC.zPGS.S2
MAF003.noMHC.zPGS.S2

我想首先在MAF子字符串上订购此列表，然后是MHC子字符串，然后是S子字符串，这样订单就是：

MAF001.incMHC.zPGS.S1
MAF001.noMHC_incRS148.zPGS.S1
MAF001.noMHC.zPGS.S1
MAF001.incMHC.zPGS.S2
MAF001.noMHC_incRS148.zPGS.S2
MAF001.noMHC.zPGS.S2
MAF002.incMHC.zPGS.S1
MAF002.noMHC_incRS148.zPGS.S1
MAF002.noMHC.zPGS.S1
MAF002.incMHC.zPGS.S2
MAF002.noMHC_incRS148.zPGS.S2
MAF002.noMHC.zPGS.S2
MAF003.incMHC.zPGS.S1
MAF003.noMHC_incRS148.zPGS.S1
MAF003.noMHC.zPGS.S1
MAF003.incMHC.zPGS.S2
MAF003.noMHC_incRS148.zPGS.S2
MAF003.noMHC.zPGS.S2

在看到关于单个子字符串的这个问题的答案之后，我已经玩过gsub： R Sort strings according to substring

但我不知道如何将这个想法扩展到字符串中的多个子串（混合字符和数字类）。

Answer 1

这是基础R中的单行：

bar <- foo[order(sapply(strsplit(foo, "\\."), function(x) paste(x[1], x[4])))]
head(data.frame(result = bar), 10)

                          result
1          MAF001.incMHC.zPGS.S1
2  MAF001.noMHC_incRS148.zPGS.S1
3           MAF001.noMHC.zPGS.S1
4          MAF001.incMHC.zPGS.S2
5  MAF001.noMHC_incRS148.zPGS.S2
6           MAF001.noMHC.zPGS.S2
7          MAF002.incMHC.zPGS.S1
8  MAF002.noMHC_incRS148.zPGS.S1
9           MAF002.noMHC.zPGS.S1
10         MAF002.incMHC.zPGS.S2

说明：

使用.：strsplit

strsplit(foo, "\\.")

提取并合并元素1和4：paste(x[1], x[4])
使用order
从foo[]

数据（foo）：

c("MAF001.incMHC.zPGS.S1", "MAF002.incMHC.zPGS.S1", "MAF003.incMHC.zPGS.S1", 
"MAF001.incMHC.zPGS.S2", "MAF002.incMHC.zPGS.S2", "MAF003.incMHC.zPGS.S2", 
"MAF001.noMHC_incRS148.zPGS.S1", "MAF002.noMHC_incRS148.zPGS.S1", 
"MAF003.noMHC_incRS148.zPGS.S1", "MAF001.noMHC_incRS148.zPGS.S2", 
"MAF002.noMHC_incRS148.zPGS.S2", "MAF003.noMHC_incRS148.zPGS.S2", 
"MAF001.noMHC.zPGS.S1", "MAF002.noMHC.zPGS.S1", "MAF003.noMHC.zPGS.S1", 
"MAF001.noMHC.zPGS.S2", "MAF002.noMHC.zPGS.S2", "MAF003.noMHC.zPGS.S2"
)

Answer 2

使用tidyr和dplyr：

library(tidyr)
library(dplyr)

df <- data.frame(filenames = c(...))

pattern = "^([^.]+)\\.([^.]+)"
df %>%
  extract(filenames, 
          into = c("maf", "mhc"), 
          regex = pattern, remove = FALSE) %>%
  arrange(maf, mhc) %>%
  select(filenames)

哪个收益

                       filenames
1          MAF001.incMHC.zPGS.S1
2          MAF001.incMHC.zPGS.S2
3           MAF001.noMHC.zPGS.S1
4           MAF001.noMHC.zPGS.S2
5  MAF001.noMHC_incRS148.zPGS.S1
6  MAF001.noMHC_incRS148.zPGS.S2
7          MAF002.incMHC.zPGS.S1
8          MAF002.incMHC.zPGS.S2
9           MAF002.noMHC.zPGS.S1
10          MAF002.noMHC.zPGS.S2
11 MAF002.noMHC_incRS148.zPGS.S1
12 MAF002.noMHC_incRS148.zPGS.S2
13         MAF003.incMHC.zPGS.S1
14         MAF003.incMHC.zPGS.S2
15          MAF003.noMHC.zPGS.S1
16          MAF003.noMHC.zPGS.S2
17 MAF003.noMHC_incRS148.zPGS.S1
18 MAF003.noMHC_incRS148.zPGS.S2

Answer 3

此结果符合您所需的输出，但只会根据b:include和MAF进行排序。我不明白如何使用S字符串进行排序，如果这个答案不能满足您的需求，请详细说明该部分。

MHC

输出是：

library(stringr)
maf <- str_extract(filenames, "MAF\\d+\\.")
mhc <- str_extract(filenames, "\\..*MHC.*\\.")
s <- str_extract(filenames, "S\\d+$")

library(magrittr)
library(dplyr)

data.frame(filenames, maf, mhc, s) %>% 
  arrange(maf, s) %>% 
  select(filenames)

其中filenames 1 MAF001.incMHC.zPGS.S1 2 MAF001.incMHC.zPGS.S2 3 MAF001.noMHC.zPGS.S1 4 MAF001.noMHC.zPGS.S2 5 MAF001.noMHC_incRS148.zPGS.S1 6 MAF001.noMHC_incRS148.zPGS.S2 7 MAF002.incMHC.zPGS.S1 8 MAF002.incMHC.zPGS.S2 9 MAF002.noMHC.zPGS.S1 10 MAF002.noMHC.zPGS.S2 11 MAF002.noMHC_incRS148.zPGS.S1 12 MAF002.noMHC_incRS148.zPGS.S2 13 MAF003.incMHC.zPGS.S1 14 MAF003.incMHC.zPGS.S2 15 MAF003.noMHC.zPGS.S1 16 MAF003.noMHC.zPGS.S2 17 MAF003.noMHC_incRS148.zPGS.S1 18 MAF003.noMHC_incRS148.zPGS.S2是

filenames

Answer 4

这里已经添加了许多好的解决方案。我添加的另一个仅基于vector的使用。

注意： OP打算对MAF，MHC和S子字符串进行排序。我坚持用这条规则对这三个人进行排序。因此，我的答案结果可能与其他答案不符。

方法：

使用regmatches在OP
使用paste根据可以执行sort
使用setNames

在名称上排序vector。

v[order(names(setNames(v, 
      paste(regmatches(v, regexpr("^MAF\\d+", v, perl = TRUE)),
            regmatches(v, regexpr("\\w*MHC\\w*", v, perl = TRUE)),
            regmatches(v, regexpr("\\w+\\d+$", v, perl = TRUE))
           ))))]
#Result
[1] "MAF001.incMHC.zPGS.S1"
[2] "MAF001.incMHC.zPGS.S2"
[3] "MAF001.noMHC.zPGS.S1"
[4] "MAF001.noMHC.zPGS.S2"
[5] "MAF001.noMHC_incRS148.zPGS.S1"
[6] "MAF001.noMHC_incRS148.zPGS.S2"
[7] "MAF002.incMHC.zPGS.S1"
[8] "MAF002.incMHC.zPGS.S2"
[9] "MAF002.noMHC.zPGS.S1"
[10] "MAF002.noMHC.zPGS.S2"
[11] "MAF002.noMHC_incRS148.zPGS.S1"
[12] "MAF002.noMHC_incRS148.zPGS.S2"
[13] "MAF003.incMHC.zPGS.S1"
[14] "MAF003.incMHC.zPGS.S2"
[15] "MAF003.noMHC.zPGS.S1"
[16] "MAF003.noMHC.zPGS.S2"
[17] "MAF003.noMHC_incRS148.zPGS.S1"
[18] "MAF003.noMHC_incRS148.zPGS.S2"

数据

v <- c("MAF001.incMHC.zPGS.S1", "MAF001.noMHC_incRS148.zPGS.S1", "MAF001.noMHC.zPGS.S1", "MAF001.incMHC.zPGS.S2", "MAF001.noMHC_incRS148.zPGS.S2", "MAF001.noMHC.zPGS.S2", "MAF002.incMHC.zPGS.S1", "MAF002.noMHC_incRS148.zPGS.S1", "MAF002.noMHC.zPGS.S1", "MAF002.incMHC.zPGS.S2", "MAF002.noMHC_incRS148.zPGS.S2", "MAF002.noMHC.zPGS.S2", "MAF003.incMHC.zPGS.S1", "MAF003.noMHC_incRS148.zPGS.S1", "MAF003.noMHC.zPGS.S1", "MAF003.incMHC.zPGS.S2", "MAF003.noMHC_incRS148.zPGS.S2", "MAF003.noMHC.zPGS.S2" )

Answer 5

我有一个专门为这样的任务设计的功能：

<强>功能

reg_sort <- function(x,...,verbose=F) {
    ellipsis <-   sapply(as.list(substitute(list(...)))[-1], deparse, simplify="array")
    reg_list <-   paste0(ellipsis, collapse=',')
    reg_list %<>% strsplit(",") %>% unlist %>% gsub("\\\\","\\",.,fixed=T)
    pattern  <-   reg_list %>% map_chr(~sub("^-\\\"","",.) %>% sub("\\\"$","",.) %>% sub("^\\\"","",.) %>% trimws)
    descInd  <-   reg_list %>% map_lgl(~grepl("^-\\\"",.)%>%as.logical)

    reg_extr <-   pattern %>% map(~str_extract(x,.)) %>% c(.,list(x)) %>% as.data.table
    reg_extr[] %<>% lapply(., function(x) type.convert(as.character(x), as.is = TRUE))

    map(rev(seq_along(pattern)),~{reg_extr<<-reg_extr[order(reg_extr[[.]],decreasing = descInd[.])]})

    if(verbose) { tmp<-lapply(reg_extr[,.SD,.SDcols=seq_along(pattern)],unique);names(tmp)<-pattern;tmp %>% print }

    return(reg_extr[[ncol(reg_extr)]])
}

数据：

vec <- c("MAF001.incMHC.zPGS.S1", "MAF002.incMHC.zPGS.S1", "MAF003.incMHC.zPGS.S1", "MAF001.incMHC.zPGS.S2", "MAF002.incMHC.zPGS.S2", "MAF003.incMHC.zPGS.S2", "MAF001.noMHC_incRS148.zPGS.S1", "MAF002.noMHC_incRS148.zPGS.S1", "MAF003.noMHC_incRS148.zPGS.S1", "MAF001.noMHC_incRS148.zPGS.S2", "MAF002.noMHC_incRS148.zPGS.S2", "MAF003.noMHC_incRS148.zPGS.S2", "MAF001.noMHC.zPGS.S1", "MAF002.noMHC.zPGS.S1", "MAF003.noMHC.zPGS.S1", "MAF001.noMHC.zPGS.S2", "MAF002.noMHC.zPGS.S2", "MAF003.noMHC.zPGS.S2" )

拨打：

reg_sort(x=vec, "^.*?(?=\\.)","(?<=\\.).*(?<=\\.S)","S\\d+$")

结果：（字符向量）

1 MAF001.incMHC.zPGS.S1 2 MAF001.incMHC.zPGS.S2 3 MAF001.noMHC.zPGS.S1 4 MAF001.noMHC.zPGS.S2 5 MAF001.noMHC_incRS148.zPGS.S1 6 MAF001.noMHC_incRS148.zPGS.S2 7 MAF002.incMHC.zPGS.S1 8 MAF002.incMHC.zPGS.S2 9 MAF002.noMHC.zPGS.S1 10 MAF002.noMHC.zPGS.S2 11 MAF002.noMHC_incRS148.zPGS.S1 12 MAF002.noMHC_incRS148.zPGS.S2 13 MAF003.incMHC.zPGS.S1 14 MAF003.incMHC.zPGS.S2 15 MAF003.noMHC.zPGS.S1 16 MAF003.noMHC.zPGS.S2 17 MAF003.noMHC_incRS148.zPGS.S1 18 MAF003.noMHC_incRS148.zPGS.S2

其他功能包括：

降序排序:(添加- infront）reg_sort(x=vec, -"^.*?(?=\\.)","(?<=\\.).*(?<=\\.S)",-"S\\d+$")

详细模式：reg_sort(x=vec, "^.*?(?=\\.)","(?<=\\.).*(?<=\\.S)","S\\d+$",verbose=T)（请参阅/检查regEx模式提取的内容以进行排序）

根据多个正则表达式子串

5 个答案: