makeFeatures-methods: getFeatures
In CMWbio/geaR: GDS Evolutionary Analysis in R

makeFeatures

R Documentation

getFeatures

Creates feature loci from a gff file

makeFeatures(
  gffName,
  feature,
  nCores = 1,
  longestIsoform,
  includeRange,
  geneIDField,
  ...
)

`gffName`	`character` Path to gff to extract features from
`feature`	`character`. Loci to import genotypes for. c("gene", "gene:exon", "gene:cds", "pseudogene", "lncRNA", "intergenic")
`nCores`	`numeric` Number of cores to run in parallel
`longestIsoform`	`logical` Only effects feature = "gene:exon". By default function will select the first entry for each gene. If `TRUE` is passed, will select the longest isoform for that gene. If there is a `"biotype"` field in the GFF it will only deal with those labeled as 'protein coding.' Selecting the longest isoform may be problematic if the `"biotype"` is missing.
`includeRange`	`GRanges` or `GRangesList` Target ranges to extract features over.
`contigMD`	`data.frame` Contig metadata. Contains two columns: `ID` with scaffold names, `length` with scaffold length. Used to select intergenic regions.
`geneIdField`	`character` Name of the gene id field in the gff, `"Name"` by default.