Map2NCBI-package: Mapping Markers to the Nearest Genomic Feature

In Map2NCBI: Mapping Markers to the Nearest Genomic Feature

Description

Allows the user to generate a list of features (gene, pseudo, RNA, CDS, and/or UTR) directly from NCBI database for any species with a build available. Option to save downloaded and formatted files is available, and the user can prioritize the feature list based on type and assembly builds present in the build used. The GetGeneList function can now handle query of the NCBI for genome builds released prior to 2018 as well as the latest build for that species. The user can then use the list of features generated or provide a list to map a set of markers (designed for SNP markers with a single base pair position available) to the closest feature based on the map build. This function does require map positions of the markers to be provided and the positions should be based on the build being queried through NCBI.

Details

Package:	Map2NCBI
Type:	Package
Version:	1.4
Date:	2020-01-23
License:	GPL (>= 2)

This package can be used as a two part process with the GetGeneList function followed by the MapMarkers function. See individual function documentation for more information.

Author(s)

Lauren L. Hulsman Hanna and David G. Riley

Maintainer: Lauren Hanna <[e-mail]>

References

Hulsman Hanna, L. L., and D. G. Riley. 2014. Mapping genomic markers to closest feature using the R package Map2NCBI. Livest. Sci. 162:59-65. doi:10.1016/j.livsci.2014.01.019

National Center for Biotechnology Information. 2018. Latest assembly version 'README' file, last updated 26 February 2018. Available at: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/README.txt (Accessed 23 Jan 2020).

See Also

Functions: GetGeneList & MapMarkers

Examples

#See individual function documentation for applied examples.

Example output

Map2NCBI documentation built on March 26, 2020, 6:23 p.m.