unite_NCBI_ac.nums: Assigns master record's id to all project records

Description Usage Arguments Details Value Author(s) Examples

Description

The function assigns the project master record's NCBI access number to all records that belong to the project.

Usage

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unite_NCBI_ac.nums(
  data,
  ac.num.var,
  title.var,
  db.var,
  type = "shotgun",
  order = TRUE,
  new.titles = FALSE
)

Arguments

data

data frame; contains information about sequence records.

ac.num.var

character; data frame variable that contains sequence accession numbers.

title.var

character; data frame variable that contains sequence titles.

db.var

character; data frame variable that contains source data base names.

type

character; type of the project which records should be united with one accession number. At the moment "shotgun" is the only possible value which corresponds to the whole genome shotgun sequencing project with shotgun technology.

order

logical; rearrange a data frame in alphabetical order of accession numbers (highly recommended).

new.titles

logical; add new titles according to new access numbers.

Details

The function looks through all records in a data frame. If the record belongs to the project (for example, WGS-project), the function assigns the project master record's NCBI access number to this record. If the record is not related to any project, it retains its own accession number.

It is highly recommended to arrange the data in alphabetical order of accession numbers, since the first record among similar ones is determined as master record.

Value

If new.titles = FALSE data frame with old and new access numbers is returned.

If new.titles = TRUE data frame with old and new access numbers and new titles is returned.

Author(s)

Elena N. Filatova

Examples

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# Example with sequences from WGS-project of Chlamydia pneumoniae genome
data (meta.target) #load metadata of target sequences with GenBank identificators
meta.target.new.ids <- unite_NCBI_ac.nums (data = meta.target,
                                          ac.num.var = meta.target$GB_AcNum,
                                          title.var = meta.target$title,
                                          db.var = meta.target$source_db,
                                          type = "shotgun", order = TRUE,
                                          new.titles = TRUE)

disprose documentation built on Jan. 24, 2022, 5:07 p.m.