probeSNPffer

[gillianmeeks]

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[bioc-issue-bot]

Hi @gillianmeeks

Thanks for submitting your package. We are taking a quick
look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: probeSNPffer
Title: Idenitifies SNPs overlapping methylation microarray probe sequences from population-specific BED file 
Version: 0.99.0
Authors@R: c(person("Shyamalika", "Gopalan", email = "[email protected]", role="aut", comment = c(ORCID = "0000-0002-2608-8472")), 
person("Gillian", "Meeks", email = "[email protected]", role=c("aut","cre"), comment = c("0000-0002-8436-6514")))
Description:This R package identifies CpG probes in a DNA methylation array dataset that overlap with known SNPs, and calculate important metrics related to these probes. Our functions do this in two steps: First, `extract.probe.regions()` takes positional, strand, and technology type information about a set of CpG probes (i.e. derived from an Illumina DNA methylation array manifest) and returns the genomic coordinates of the entire probe region in [BED format (https://genome.ucsc.edu/FAQ/FAQformat.html). Second, `flag.overlap()` takes the BED file generated in the previous step, along with a BED file containing SNPs to be queried, and returns their intersection.
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports: 
    GenomicRanges,
    S4Vectors
Depends: 
    R (>= 2.10)
LazyData: true
Suggests: 
    knitr,
    rmarkdown,
    tibble,
    dplyr,
    ggplot2
VignetteBuilder: knitr
biocViews: DNAMethylation, Microarray, Annotation, Genetics
BugReports: https://github.com/gillianmeeks/probeSNPffer/issues