Description Usage Arguments Details Value See Also Examples
View source: R/locus.from.rsid.R
Import SNPs from rsid for use in motifbreakR
1 | snps.from.rsid(rsid = NULL, dbSNP = NULL, search.genome = NULL)
|
rsid |
Character; a character vector of rsid values from dbSNP |
dbSNP |
an object of class SNPlocs to lookup rsids; see |
search.genome |
an object of class BSgenome for the species you are interrogating;
see |
snps.from.rsid
take an rsid, or character vector of rsids and
generates the required object to input into motifbreakR
a GRanges object containing:
SNP_id |
The rsid of the snp with the "rs" portion stripped |
alleles_as_ambig |
THE IUPAC ambiguity code between the reference and alternate allele for this SNP |
REF |
The reference allele for the SNP |
ALT |
The alternate allele for the SNP |
See motifbreakR
for analysis; See snps.from.file
for an alternate method for generating a list of variants.
1 2 3 4 5 6 7 | library(BSgenome.Hsapiens.UCSC.hg19)
library(SNPlocs.Hsapiens.dbSNP142.GRCh37)
snps.file <- system.file("extdata", "pca.enhancer.snps", package = "motifbreakR")
snps <- as.character(read.table(snps.file)[,1])
snps.mb <- snps.from.rsid(snps[1],
dbSNP = SNPlocs.Hsapiens.dbSNP142.GRCh37,
search.genome = BSgenome.Hsapiens.UCSC.hg19)
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