Target factory for GFF/GTF features metadata import — import_fmetadata_gff

Creates a list of targets that track each file and import the features metadata from each GFF/GTF file.

Usage

import_fmetadata_gff_factory(
  files,
  feature_types,
  add_fieldss,
  target_name_suffixes
)

Arguments

files: Character vector, vector of paths to the samples metadata GFF or GTF files.
feature_types: Character vector, the type of features to extract from each annotation file. Currently supports 'genes' and 'transcripts'.
add_fieldss: List, where each element is a character vector of field names in each GFF/GTF file to extract that are not imported by default. If a character vector is provided, will be used for all files to read in.
target_name_suffixes: Character vector, a suffix to add to the name of the targets created by this target factory for each dataset.

Value

A list of target objects. For example, with two files to import and target_name_suffixes = c("geno", "transcripto"), the factory returns the following targets:

fmetadata_file_geno and fmetadata_file_transcripto: targets tracking the genomics and transcriptomics annotation files, respectively.
fmetadata_geno and fmetadata_transcripto: targets that import the genomics and transcriptomics features metadata datasets, respectively.

Examples

if (FALSE) { # \dontrun{
## in the _targets.R
library(moiraine)

list(
  import_fmetadata_gff_factory(
    c(
      "data/annotation.gff",
      "data/annotationv2.gtf"
    ),
    feature_types = c("genes", "transcripts"),
    add_fieldss = list(
      c("gene_name", "gene_custom_ID"),
      c("transcript_name")
    ),
    target_name_suffixes = c("geno", "transcripto")
  )
)
} # }