Get NOISeq::readData ready annotations

A convenience function to make a data frame containing biological annotations required by NOISeq to run NOISeq::readData function using custom GTF/GFF file and FASTA.

Usage

easyNOISeqAnnot(
  gff,
  fasta,
  name = "Tgondii",
  select = c("protein_coding_gene", "ncRNA_gene", "pseudogene"),
  geneidcol = "ID",
  genetype = "ebi_biotype"
)

Arguments

gff

A link to GFF file from VEuPathDB or path to GTF file produced using AGAT.

fasta

A link or path to the genome fasta file.

name

Name of the organism.

select

Type of features to be selected. By default we select "protein_coding_gene","ncRNA_gene"and "pseudogene" as they cover all the genes in the VEuPathDB annotation files. If using AGAT formatted GTF file, using "gene" would be sufficient as AGAT put all the genes types under gene tag.

geneidcol

Use the tag that refers to the gene IDs in the GTF/GFF file.

genetype

Use the tag that refers to the gene subtypes such as "ebi_biotype".

Value

A dataframe containing annotations per gene such as GC content, gene description, gene-length, gene start, gene end coordinates and chromosome information.

Examples

if (FALSE) { # \dontrun{
 df <- easyNOISeqAnnot(
 gff="https://toxodb.org/common/downloads/release-68/EpraecoxHoughton/gff/data/ToxoDB-68_EpraecoxHoughton.gff",
 fasta = "https://toxodb.org/common/downloads/release-68/EpraecoxHoughton/fasta/data/ToxoDB-68_EpraecoxHoughton_Genome.fasta")


} # }