| LM_eukaryotes {LifemapR} | R Documentation |
Transformation in a LifemapR format of NCBI information for 1000 eukaryotes
Description
A dataset containing NCBI information of 1000 eukaryotes. The variables are as follows:
Usage
data(LM_eukaryotes)
Format
A lifemap object - a list containing the basemap used to fetch data and df, a data frame with 2760 rows and 26 variables:
- X.Organism.Name
Organism name at the species level
- taxid
NCBI taxid
- BioProject.Accession
BioProject Accession number (from BioProject database)
- BioProject.ID
BioProject ID
- Group
Commonly used organism groups: Animals, Fungi, Plants, Protists
- SubGroup
NCBI Taxonomy level below group: Mammals, Birds, Fishes, Flatworms, Insects, Amphibians, Reptiles, Roundworms, Ascomycetes, Basidiomycetes, Land Plants, Green Algae, Apicomplexans, Kinetoplasts
- Size..Mb.
Total length of DNA submitted for the project
- GC.
Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the project
- Assembly.Accession
Name of the genome assembly (from NCBI Assembly database)
- Replicons
Number of replicons in the assembly
- WGS
Four-letter Accession prefix followed by version as defined in WGS division of GenBank/INSDC
- Scaffolds
Number of scaffolds in the assembly
- Genes
Number of Genes annotated in the assembly
- Proteins
Number of Proteins annotated in the assembly
- Release.Date
First public sequence release for the project
- Modify.Date
Sequence modification date for the project
- Status
Highest level of assembly:
Chromosomes: one or more chromosomes are assembled
Scaffolds or contigs: sequence assembled but no chromosomes- Center
Origin of the sample
- BioSample.Accession
BioSample Accession number
- lon
longitude of taxids on a specific basemap
- lat
latitude of taxids on a specific basemap
- sci_name
scientific name of taxids
- zoom
zoom of taxids on a specific basemap
- ascend
the list of all ancestors of taxids on a specific basemap
- type
either "requested" if the taxid was given, "ancestor" if gotten from the database
- ancestor
the direct ancestor oftaxids on a specific basemap