Map2NCBI: Mapping Markers to the Nearest Genomic Feature

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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 current 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 current build used. 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.

Author
Lauren L. Hulsman Hanna and David G. Riley
Date of publication
2015-11-13 08:55:43
Maintainer
Lauren Hanna <Lauren.Hanna@ndsu.edu>
License
GPL (>= 2)
Version
1.1

View on CRAN

Man pages

Example10MarkerFile
Example Marker File with 10 Markers on BTA 1
GeneList_BTA1
Output from GetGeneList function for BTA 1
GetGeneList
A Function to Filter and Save Genomic Features from NCBI
Map2NCBI-package
Mapping Markers to the Nearest Genomic Feature
MapMarkers
Mapping SNP Markers to Closest Genomic Feature

Files in this package

Map2NCBI
Map2NCBI/NAMESPACE
Map2NCBI/data
Map2NCBI/data/Example10MarkerFile.rda
Map2NCBI/data/GeneList_BTA1.rda
Map2NCBI/R
Map2NCBI/R/MapMarkers.R
Map2NCBI/R/GetGeneList.R
Map2NCBI/MD5
Map2NCBI/DESCRIPTION
Map2NCBI/man
Map2NCBI/man/Map2NCBI-package.Rd
Map2NCBI/man/MapMarkers.Rd
Map2NCBI/man/GeneList_BTA1.Rd
Map2NCBI/man/Example10MarkerFile.Rd
Map2NCBI/man/GetGeneList.Rd