Regex 用r中的条件替换数据帧中字符串的部分
我有这样一个数据框:Regex 用r中的条件替换数据帧中字符串的部分,regex,r,dna-sequence,Regex,R,Dna Sequence,我有这样一个数据框: df = read.table(text="REF Alt S00001 S00002 S00003 S00004 S00005 TAAGAAG TAAG TAAGAAG/TAAGAAG TAAGAAG/TAAG TAAG/TAAG TAAGAAG/TAAGAAG TAAGAAG/TAAGAAG T TG T/T -/- TG/TG T/T T/T CAAAA CAAA CAAAA/CAAAA CAAAA/CAAA
df = read.table(text="REF Alt S00001 S00002 S00003 S00004 S00005
TAAGAAG TAAG TAAGAAG/TAAGAAG TAAGAAG/TAAG TAAG/TAAG TAAGAAG/TAAGAAG TAAGAAG/TAAGAAG
T TG T/T -/- TG/TG T/T T/T
CAAAA CAAA CAAAA/CAAAA CAAAA/CAAA CAAAA/CAAAA -/- CAAAA/CAAAA
TTGT TTGTGT TTGT/TTGT TTGT/TTGT TTGT/TTGT TTGTGT/TTGTGT TTGT/TTGTGT
GTTT GTTTTT GTTT/GTTTTT GTTT/GTTT GTTT/GTTT GTTT/GTTT GTTTTT/GTTTTT", header=T, stringsAsFactors=F)
我想根据“REF”和“Alt”列中字符串的长度,将“/”分隔的字符元素替换为“D”或“I”。如果这些元素与最长的元素匹配,它们将替换为“I”,否则替换为“D”。但“一”字不变。因此,预期结果如下:
REF Alt S00001 S00002 S00003 S00004 S00005
TAAGAAG TAAG I/I I/D D/D I/I I/I
T TG D/D -/- I/I D/D D/D
CAAAA CAAA I/I I/D I/I -/- I/I
TTGT TTGTGT D/D D/D D/D I/I D/I
GTTT GTTTTT D/I D/D D/D D/D I/I
您可以使用
REF
和Alt
的所有组合以及I
和D
的相应组合创建地图:
refalt <- data.frame(
from=c(df$REF, df$Alt),
to=c(rep('I', length(df$REF)), rep('D', length(df$Alt))),
stringsAsFactors=FALSE)
refalt <- rbind(refalt, c('-', '-'))
from <- expand.grid(refalt$from, refalt$from)
to <- expand.grid(refalt$to, refalt$to)
map <- paste(to[,1], to[,2], sep='/')
names(map) <- paste(from[,1], from[,2], sep='/')
refalt这里有一种方法。我使用了stringi
包,因为它可以很好地处理模式向量和字符串向量以进行搜索
首先确定哪个字符串较短,哪个字符串较长:
short <- ifelse(nchar(df$Alt) > nchar(df$REF), df$REF, df$Alt)
long <- ifelse(nchar(df$REF) > nchar(df$Alt), df$REF, df$Alt)
短nchar(df$REF)、df$REF、df$Alt)
长nchar(df$Alt)、df$REF、df$Alt)
使用这些选项并在列上循环,根据需要指定替换项。首先替换长模式,以避免出现与短模式和长模式匹配的字符串问题:
library(stringi)
df[,!(names(df) %in% c("REF", "Alt"))] <- # assign into original df
lapply(1:(ncol(df) - 2), # - 2 because there are two columns we don't use
function(ii) stri_replace_all_fixed(df[ ,ii + 2], long, "I")) # + 2 to skip first 2 columns
df[,!(names(df) %in% c("REF", "Alt"))] <-
lapply(1:(ncol(df) - 2),
function(ii) stri_replace_all_fixed(df[ ,ii + 2], short, "D"))
# REF Alt S00001 S00002 S00003 S00004 S00005
#1 TAAGAAG TAAG I/I I/D D/D I/I I/I
#2 T TG D/D -/- I/I D/D D/D
#3 CAAAA CAAA I/I I/D I/I -/- I/I
#4 TTGT TTGTGT D/D D/D D/D I/I D/I
#5 GTTT GTTTTT D/I D/D D/D D/D I/I
库(stringi)
df[,!(名称(df)%in%c(“REF”,“Alt”))]
library(stringi)
df[,!(names(df) %in% c("REF", "Alt"))] <- # assign into original df
lapply(1:(ncol(df) - 2), # - 2 because there are two columns we don't use
function(ii) stri_replace_all_fixed(df[ ,ii + 2], long, "I")) # + 2 to skip first 2 columns
df[,!(names(df) %in% c("REF", "Alt"))] <-
lapply(1:(ncol(df) - 2),
function(ii) stri_replace_all_fixed(df[ ,ii + 2], short, "D"))
# REF Alt S00001 S00002 S00003 S00004 S00005
#1 TAAGAAG TAAG I/I I/D D/D I/I I/I
#2 T TG D/D -/- I/I D/D D/D
#3 CAAAA CAAA I/I I/D I/I -/- I/I
#4 TTGT TTGTGT D/D D/D D/D I/I D/I
#5 GTTT GTTTTT D/I D/D D/D D/D I/I