snp_info {kangar00}

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 signature 'character'
snp_info(x)

## S4 method for signature 'snp_info'
show(object)

## S4 method for signature '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

Author(s)

Stefanie Friedrichs

See Also

pathway_info, get_anno

Examples

data(rs10243170_info) # snp_info("rs10243170")

rs10243170_info
summary(rs10243170_info)