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 >> S         


        

Answer 1

Escape " with backslash \. So you will have:

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