Map2NCBI: Mapping Markers to the Nearest Genomic Feature
Version 1.1

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.

AuthorLauren L. Hulsman Hanna and David G. Riley
Date of publication2015-11-13 08:55:43
MaintainerLauren Hanna <Lauren.Hanna@ndsu.edu>
LicenseGPL (>= 2)
Version1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Map2NCBI")

Getting started

Package overview

Popular 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
See all...

All man pages Function index File listing

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

Functions

Example10MarkerFile Man page
GeneList_BTA1 Man page
GetGeneList Man page Source code
Map2NCBI Man page
Map2NCBI-package Man page
MapMarkers Man page Source code

Files

NAMESPACE
data
data/Example10MarkerFile.rda
data/GeneList_BTA1.rda
R
R/MapMarkers.R
R/GetGeneList.R
MD5
DESCRIPTION
man
man/Map2NCBI-package.Rd
man/MapMarkers.Rd
man/GeneList_BTA1.Rd
man/Example10MarkerFile.Rd
man/GetGeneList.Rd
Map2NCBI documentation built on May 19, 2017, 1:34 p.m.

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