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  • How can I extract sequence name from fast file in R

    Here is my code:
    Code:
    setwd("/Users/xshang/Dropbox/project-ing/peptidome")
    library("Biostrings")
    human_protein <- readAAStringSet("HUMAN.fasta",use.names=TRUE)
    When I use
    Code:
    names(human_protein[[1]])
    , it returns "NULL". How can I extract sequence name from fast file in R?

    Thanks!

  • #2
    Try
    Code:
    names(human_protein)[1]
    The names() function is an accessor for the names in the AAStringSet object and returns a character vector. Alternatively, you can also use
    Code:
    names(human_protein[1])
    The [ function also returns an AAStringSet, rather than an AAString (returned by [[).

    Comment


    • #3
      Originally posted by dpryan View Post
      Try
      Code:
      names(human_protein)[1]
      The names() function is an accessor for the names in the AAStringSet object and returns a character vector. Alternatively, you can also use
      Code:
      names(human_protein[1])
      The [ function also returns an AAStringSet, rather than an AAString (returned by [[).
      It works! Many thanks!

      Comment

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