Overload #6
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Overload #6
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c-mertes
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Feb 1, 2022
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It looks good. And it is definitely better now with the overloading.
Just one question on top: there is a lot of casting happening. Do we really want this? I would assume, if you pass a GRange object you want this back and if you pass on a data.table you want the same object back.
R/add_gnomAD_AF.R
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| #' @examples | ||
| #' \dontrun{ | ||
| #' BiocManager::install("MafDb.gnomAD.r2.1.hs37d5") | ||
| #' file <- system.file("extdata", "allelic_counts_HG00187.csv", package = "tMAE", mustWork = TRUE) | ||
| #' maeCounts <- fread(file) | ||
| #' maeRes <- DESeq4MAE(maeCounts) | ||
| #' genome_assembly <- 'hg19' | ||
| #' res <- add_gnomAD_AF(maeRes, genome_assembly = genome_assembly, pop="AF") | ||
| #' } | ||
| #' |
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I would keep the documentation all together when setting the genetic function. In addition, you rather use the exome data and run the example. This way we make sure the examples work.
| gr <- GRanges(seqnames = object$contig, | ||
| ranges = IRanges(start=object$position, width=1), | ||
| strand = '*') | ||
| # score the gr |
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rather call here add_gnomad_AF with your GRange object. This way you have the same logic for all input data and don't duplicate code.
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