bioc-issue-bot
commented
1 month ago 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 = "shyamie@gmail.com", role="aut", comment = c(ORCID = "0000-0002-2608-8472")),
person("Gillian", "Meeks", email = "glmeeks@ucdavis.edu", 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
lshep
gillianmeeks
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