annotate_probes: Annotate probes

In disprose: Discriminating Probes Selection

Annotate probes

Description

Get genome annotation for oligonucleotide sequence

Usage

annotate_probes(
  source = "data.frame",
  ann.data = NULL,
  gff.path = NULL,
  org.name,
  db = "refseq",
  refs = TRUE,
  probe.id.var,
  probe.start.var,
  probe.stop.var,
  file.annot = NULL,
  save.format = "txt",
  sep = ";",
  return = "add.resume",
  priority = c("CDS", "gene", "region"),
  data,
  data.probe.id.var,
  delete.downloads = FALSE,
  verbose = TRUE
)

Arguments

source	character; genome annotation source. Possible values are: "data.frame" (from data frame), "giff" (from GIFF file), "load" (download from NCBI with getGFF function)
ann.data	genome annotation data frame
gff.path	character; .gff file name and path
org.name	character; the scientific name of the organism of interest
db	character; database from which the genome shall be retrieved; possible values are "refseq", "genbank", "ensembl"
refs	logical; download genome if it isn't marked in the database as either a reference or a representative genome
probe.id.var	vector of probes' identification numbers
probe.start.var, probe.stop.var	integer; vector of probes' start and end coordinates
file.annot	character; resulting annotation file name and path
save.format	character; format of resulting annotation file; possible values are "txt", "csv"
sep	character; field separator string
return	character; returned object; possible values are: "annotation" (annotation data frame), "resume" (annotation attributes only), "add.resume" (user's data frame with added annotation attributes)
priority	character; vector of sequence ontology types that should be returned in resume in the first place
data, data.probe.id.var	users data frame and probes' identification variable in it (used if return = "add.resume")
delete.downloads	logical; delete files that were downloaded from NCBI
verbose	logical; show messages

Details

This function uses boimartr genome annotation retrieval instruments. See getGFF for details. If retrieval is not available, GFF file may be used.

This function creates annotation ".txt" or ".csv" file. By default file is created in working directory. Optionally function returns annotation resume, i.e. annotation attribute for specified sequence ontology (SO). Priorities of SOs are set by user in priopity parameter. For example, if priopity = c("CDS", "gene", "region"), the function returns resume for "CDS" SO, if there are none - for "gene" CO etc. If there are several attributes meet priority, the first annotation attribute is returned. If none of priority COs found, the first annotation attribute is returned.

Number of found annotations are indicated in returned data ("ann.n" column).

Value

Annotation data frame, or annotation attributes, or user's data frame with added annotation attributes. Also annotation file is created.

Author(s)

Elena N. Filatova

Examples

path<-tempdir()
dir.create(path) # create temporal directory
data(ann.data) # load genome annotation data frame
annotation<-annotate_probes(source = "data.frame", ann.data = ann.data,
                probe.id.var = 1:5,
                probe.start.var = c (1, 100, 200, 300, 400),
                probe.stop.var = c (99, 199, 299, 399, 499),
                file.annot = paste0(path, "/annotation.txt"), save.format = "txt",
                return = "resume")
file.remove(paste0(path, "/annotation.txt")) # delete files
unlink(path, recursive = TRUE)

disprose documentation built on March 19, 2022, 2:15 a.m.