regex - Subset all 3 digit numbers and collapse them with a separator in a data frame. R -


i'm formating data set each entry has adegenet format codominant markers, such as:

loci1 ###/### 208/210 200/204 198/208

where # represents digit (the number allele size in basepairs). data has homozygous entries (all 3 digit integers no separator) have the form of:

loci1 ### 208 198

i intend paste 3 digit string sep='/' produce first format. i've tried use grep subset these homozygous entries finding non ###/### , negating match using table matching such as:

a <- grep('\\b\\d{3}?[/]\\d{3}', score$loci1, value =t )  # subset ###/###/ score[!(a %in% 1:nrow(score$loci1)), ] # works on vectors...

after subset paste. problem arises when apply data frame. grep seems treat data frame list (which in part is) , returns columns have match.

so in short how can go ### ###/### in data frame

self contained example of data:

score2 <- null set.seed(9) loci1 <- null loci2 <- null loci3 <- null (i in 1:5) loci1 <- append(loci1, paste(sample(seq(from = 230, to=330,  by=3), 2, replace = f), collapse = '/')) (i in 1:5) loci2 <- append(loci2, paste(sample(seq(from = 230, to=330, by=3), 2, replace = f), collapse = '/')) (i in 1:5) loci3 <- append(loci3, paste(sample(seq(from = 230, to=330, by=3), 2, replace = f), collapse = '/'))  score2 <- data.frame(loci1, loci2, loci3, stringsasfactors = f) score2[2,3] <- strsplit(score2[2,3], split = '/')[1] score2[5,2] <- strsplit(score2[3,3], split = '/')[1] score2[1,1] <- strsplit(score2[1,1], split = '/')[1] score2[c(1, 4),c(2,3)] <- na score2

you replace 3 digit items separator , copy:

 sub("^(...)$", "\\1/\\1", loci1)

use lapply anonymized function:

data.frame( lapply(score2, function(x) sub("^(...)$", "\\1/\\1", x)  ) )     loci1   loci2   loci3 1 251/251    <na>    <na> 2 251/329 320/257 260/260 3 275/242 278/329 281/320 4 269/266    <na>    <na> 5 296/326 281/281 326/314

(not sure "paste-part" supposed refer to, think intent of question)

if numeric values have varying number of digits use pattern argument "^([0-9]{1,9})$"


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