R 按部分字符串匹配分组
我有一个表,其中有一个类别列表,每个类别都有一个计数值,我想根据相似性对其进行折叠。。。例如,水手-1_Amel和水手-10将是一个单一的水手类别,任何名字中带有“骑师”或“帽子”的东西都应该折叠起来 我正在努力寻找一个能够应对所有可能性的解决方案。是否有简单的dplyr解决方案 可复制R 按部分字符串匹配分组,r,dplyr,tidyverse,base,R,Dplyr,Tidyverse,Base,我有一个表,其中有一个类别列表,每个类别都有一个计数值,我想根据相似性对其进行折叠。。。例如,水手-1_Amel和水手-10将是一个单一的水手类别,任何名字中带有“骑师”或“帽子”的东西都应该折叠起来 我正在努力寻找一个能够应对所有可能性的解决方案。是否有简单的dplyr解决方案 可复制 > dput(tibs) structure(list(type = c("(TTAAG)n_1", "AMARI_1", "Copia-4_LH-I", "DNA", "DNA-1_CQ", "DNA
> dput(tibs)
structure(list(type = c("(TTAAG)n_1", "AMARI_1", "Copia-4_LH-I",
"DNA", "DNA-1_CQ", "DNA/hAT-Charlie", "DNA/hAT-Tip100", "DNA/MULE-MuDR",
"DNA/P", "DNA/PiggyBac", "DNA/TcMar-Mariner", "DNA/TcMar-Tc1",
"DNA/TcMar-Tigger", "G3_DM", "Gypsy-10_CFl-I", "hAT-1_DAn", "hAT-16_SM",
"hAT-N4_RPr", "HELITRON7_CB", "Jockey-1_DAn", "Jockey-1_DEl",
"Jockey-12_DF", "Jockey-5_DTa", "Jockey-6_DYa", "Jockey-6_Hmel",
"Jockey-7_HMM", "Jockey-8_Hmel", "LINE/Dong-R4", "LINE/I", "LINE/I-Jockey",
"LINE/I-Nimb", "LINE/Jockey", "LINE/L1", "LINE/L2", "LINE/R1",
"LINE/R2", "LINE/R2-NeSL", "LINE/Tad1", "LTR/Gypsy", "Mariner_CA",
"Mariner-1_AMel", "Mariner-10_HSal", "Mariner-13_ACe", "Mariner-15_HSal",
"Mariner-16_DAn", "Mariner-19_RPr", "Mariner-30_SM", "Mariner-39_SM",
"Mariner-42_HSal", "Mariner-46_HSal", "Mariner-49_HSal", "TE-5_EL",
"Unknown", "Utopia-1_Crp"), n = c(1L, 1L, 1L, 2L, 1L, 18L, 3L,
9L, 2L, 8L, 21L, 12L, 18L, 1L, 3L, 1L, 2L, 2L, 1L, 1L, 1L, 1L,
1L, 2L, 1L, 2L, 1L, 2L, 7L, 2L, 7L, 24L, 1L, 1L, 5L, 3L, 1L,
1L, 7L, 1L, 5L, 1L, 1L, 5L, 5L, 1L, 1L, 3L, 5L, 5L, 2L, 1L, 190L,
1L)), row.names = c(NA, -54L), class = c("tbl_df", "tbl", "data.frame"
))
如果没有通用性来定义组,您可以在时使用
case\u来定义单个条件
library(dplyr)
library(stringr)
tibs %>%
mutate(category = case_when(str_detect(type, 'Mariner-\\d+') ~ 'Mariner',
str_detect(type, 'Jockey|hAT') ~ 'common',
#Add more conditions
))
在我看来,您更广泛的类型大多/完全在字符串的开头。因此,您可以仅使用该类型的第一个字母数字序列([[:alnum:]+
)作为更广泛的类型。这将为您提供以下类型:
library(tidyverse)
df %>%
mutate(type_short = str_extract(type, "[[:alnum:]]+")) %>%
count(type_short, sort = TRUE)
#> # A tibble: 15 x 2
#> type_short n
#> <chr> <int>
#> 1 Mariner 12
#> 2 LINE 11
#> 3 DNA 10
#> 4 Jockey 8
#> 5 hAT 3
#> 6 AMARI 1
#> 7 Copia 1
#> 8 G3 1
#> 9 Gypsy 1
#> 10 HELITRON7 1
#> 11 LTR 1
#> 12 TE 1
#> 13 TTAAG 1
#> 14 Unknown 1
#> 15 Utopia 1
理论上,您也可以尝试在这里使用字符串相似性。然而,你们的类型之间并没有太大的相似性。例如,相对Levenshtein距离(较长字符串的距离/字符)检索如下结果:
strings <- c("Mariner-1_Amel", "Mariner-10")
adist(strings) / max(nchar(strings))
#> [,1] [,2]
#> [1,] 0.0000000 0.3571429
#> [2,] 0.3571429 0.0000000
字符串[,1][,2]
#> [1,] 0.0000000 0.3571429
#> [2,] 0.3571429 0.0000000
这可以解释为这两种类型有36%的相似性。在这种情况下,找到一个好的阈值可能很难。此解决方案在
时使用包dplyr
函数case\u和基Rgrepl
library(dplyr)
tibs %>%
mutate(category = case_when(
grepl("hAT|Jockey", type) ~ "Jokey",
grepl("Mariner", type) ~ "Mariner",
grepl("DNA", type) ~ "DNA",
grepl("LINE", type) ~"LINE",
TRUE ~ as.character(type)
),
category = factor(category)
)
这些是你唯一想崩溃的吗?不理论上还有更多的组合。。。
library(dplyr)
tibs %>%
mutate(category = case_when(
grepl("hAT|Jockey", type) ~ "Jokey",
grepl("Mariner", type) ~ "Mariner",
grepl("DNA", type) ~ "DNA",
grepl("LINE", type) ~"LINE",
TRUE ~ as.character(type)
),
category = factor(category)
)