kangar00 (version 1.4)

snp_info: An S4 class for an object assigning SNP positions to rs-numbers (for internal use)

Description

An S4 class for an object assigning SNP positions to rs-numbers (for internal use)

This function gives for a vector of SNP identifiers the position of each SNP as extracted from the Ensemble database. The database is accessed via the R-package biomaRt.

show Shows basic information on snp_info object

summary Summarizes information on snp_info object

Usage

snp_info(x, ...)
# S4 method for character
snp_info(x)
# S4 method for snp_info
show(object)
# S4 method for snp_info
summary(object)

Arguments

x

A character vector of SNP rsnumbers for which positions will be extracted.

...

further arguments can be added.

object

An object of class snp_info.

Value

A data.frame including the SNP positions with columns 'chromosome', 'position' and 'snp'. SNPs not found in the Ensemble database will not be listed in the returned snp_info object, SNPs with multiple positions will appear several times.

show Basic information on snp_info object.

summary Summarized information on snp_info object.

Slots

info

A data.frame including information on SNP positions

See Also

pathway_info, get_anno

Examples

# NOT RUN {
data(rs10243170_info) # snp_info("rs10243170")

rs10243170_info
summary(rs10243170_info)
# }