package: Full genome sequences for Homo sapiens (UCSC version hg38,...

In Jfortin1/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major: Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected major alleles (dbSNP151)

Description

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with major allele injected from dbSNP151, and stored in Biostrings objects. Only single nucleotide variants (SNVs) were considered. At each SNV, the most frequent allele was chosen at the major allele to be injected into the reference genome.

Author(s)

Jean-Philippe Fortin

See Also

• BSgenome objects and the available.genomes function in the BSgenome software package.

• DNAString objects in the Biostrings package.

• The BSgenomeForge vignette (vignette("BSgenomeForge")) in the BSgenome software package for how to make a BSgenome data package.

Examples

BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major
genome_maj <- BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major
head(seqlengths(genome_maj))

# Getting nucleotide at SNP rs12813551 (C/T, MAF>0.5)
# Major allele genome has a T:
chr <- "chr12"
pos <- 25241845L
getSeq(genome_maj, chr, start=pos, end=pos)

# Reference genome has the minor allele, C:
if (require(BSgenome.Hsapiens.UCSC.hg38)){
    genome_ref <- BSgenome.Hsapiens.UCSC.hg38
    getSeq(genome_ref, chr, start=pos, end=pos)
}

# Minor allele genome agrees with reference genome (C):
if (require(BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor)){
    genome_min <- BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor
    getSeq(genome_min, chr, start=pos, end=pos)
}

Jfortin1/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major documentation built on Dec. 18, 2021, 1:28 a.m.