annotateSNPs: Annotate SNPs

In solarius: An R Interface to SOLAR

Description

The function annotates SNPs based on NCBI2R R package, in particular AnnotateSNPList function.

Usage

annotateSNPs(x, mode = c("significant", "top", "all"), alpha = 0.05,
  num.top = 10, query.size = 500, verbose = 0)

Arguments

x	An object of class solarAssoc or a character vector of SNPs.
mode	A character with the mode of SNPs selection. Possible values are "significant", "top" and "all". The default value is "significant".
alpha	A numeric value from 0 to 1, the significance level after Bonferroni multiple-test correction. Corresponds to mode equal to "significant".
num.top	An integer value, the number of top SNPs to be annotated. Corresponds to mode equal to "top". The default value is 10.
query.size	An integer, the maximum number of SNPs allowed for a single query to the NCBI database. The default value is 500. See also the help page for NCBI_snp_query function in rsnps package. If the number of SNPs is greater than query.size, then the query is split into batches automatically.
verbose	An integer, the verbose level. The default value is 0.
...	Additional arguments.

Details

See https://ncbi2r.wordpress.com/ for more details.

Value

A data table with annotation results.

solarius documentation built on May 2, 2019, 2:43 a.m.