Adding ' " ' quote inside a paste command in R

Question

I'm trying to have " (double quote) inside a pasted command in R

paste("perl -ane 'system("cat /auto/Sample_output/tmp.$F[0].vcf >> Sample_90061.vcf");'",sep="")

it says

Error: unexpected symbol in "paste("perl -ane 'system("cat"

I tried to create the quoted part alone and then paste it by

complicated = paste('"cat /auto/Sample_output/tmp.$F[0].vcf >> Sample_90061.vcf"',sep="")

but it shows as

> complicated
[1] "\"cat /auto/Sample_output/tmp.$F[0].vcf >> Sample_90061.vcf\""

Can somebody help me to solve this issue?

to put " in ". you use \" for instance: "The boy said, \"Hello World!\"" — u8sand, Jan 07 '13 at 23:32
`shQuote`, `sQuote`, and `dQuote` might be functions to look into as well. — Dason, Jan 08 '13 at 02:13

score 4 · Accepted Answer · answered Jan 07 '13 at 23:34

4

Escape " with backslash \. So you will have:

paste("perl -ane 'system(\"cat /auto/Sample_output/tmp.$F[0].vcf >> Sample_90061.vcf\");'",sep="")

answered Jan 07 '13 at 23:34

Adam Stelmaszczyk

1

Yes. Sometimes it possible to include `"` if the string is enclosed in single-quotes, but didn't try it here since this answer is "more correct". – IRTFM Jan 08 '13 at 04:59

1 Answers1