Use ensembl database server instead of biomart

man/chromosomes.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{chromosomes}
+\alias{chromosomes}
+\title{Information on chromosomes for each included species.}
+\format{
+A \link{data.table} with the following columns:
+\describe{
+\item{species}{Species ID}
+\item{id}{Chromosome ID, theses are Ensembl sequence IDs}
+\item{name}{Chromosome name}
+\item{length}{Length in base pairs}
+}
+}
+\usage{
+chromosomes
+}
+\description{
+Information on chromosomes for each included species.
+}
+\keyword{datasets}

man/distances.Rd

@@ -9,7 +9,7 @@ A \link{data.table} with the following columns:
 \describe{
 \item{species}{Species ID}
 \item{gene}{Gene ID}
-\item{chromosome_name}{Chromosome name from the specified species}
+\item{chromosome}{Chromosome ID}
 \item{start_position}{Start position in base pairs}
 \item{end_position}{End position in base pairs}
 \item{distance}{Computed distance to nearest telomere}

man/genes.Rd

@@ -9,7 +9,7 @@ A \link{data.table} with the following columns:
 \describe{
 \item{id}{Ensembl gene ID}
 \item{name}{The gene's HGNC name (if available)}
-\item{chrosome}{The human chromosome the gene is located on}
+\item{chromosome}{The human chromosome the gene is located on}
 }
 }
 \usage{

man/species.Rd

@@ -7,8 +7,10 @@
 \format{
 A \link{data.table} with the following columns:
 \describe{
-\item{id}{Unique species ID}
+\item{id}{Unique species ID, these are NCBI taxon IDs}
 \item{name}{Human readable species name}
+\item{scientific_name}{Scientific name of the species}
+\item{table_name}{Table name within the Ensembl database}
 \item{n_chromosomes}{Number of chromosomes}
 \item{median_chromosome_length}{Median length of chromosomes}
 }