annotateSNPs

An object of class <code>solarAssoc</code> or a character vector of SNPs.

A character with the mode of SNPs selection.
Possible values are <code>"significant"</code>, <code>"top"</code> and <code>"all"</code>.
The default value is <code>"significant"</code>.

mode

A numeric value from 0 to 1, the significance level after Bonferroni multiple-test correction.
Corresponds to <code>mode</code> equal to <code>"significant"</code>.

alpha

An integer value, the number of top SNPs to be annotated.
Corresponds to <code>mode</code> equal to <code>"top"</code>.
The default value is 10.

num.top

Logical, indicates whether to capture the output from <code>AnnotateSNPList</code> function.
The default value is FALSE.

capture.output

The function annotates SNPs based on <code>NCBI2R</code> R package,
in particular <code>AnnotateSNPList</code> function.


  SOLAR is the standard software program to perform linkage and association mappings 
  of the quantitative trait loci (QTLs) in pedigrees of arbitrary size and complexity.
  This package allows the user to exploit the variance component methods implemented in SOLAR.
  It automates such routine operations as formatting pedigree and phenotype data.
  It also parses the model output and contains summary and plotting functions for exploration of the results.
  In addition, solarius enables parallel computing of the linkage and association analyses,
  that makes the calculation of genome-wide scans more efficient.
  See <http://solar.txbiomedgenetics.org/> for more information about SOLAR.

annotateSNPs: Annotate SNPs

Description

Usage

Arguments

Value

Details