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Merge pull request #106 from azodichr/splatPop
Add the splatPop simulation, an extension to splat that includes eQTLs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| #' @rdname newParams | ||
| #' @importFrom methods new | ||
| #' @export | ||
| newSplatPopParams <- function(...) { | ||
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| for (pkg in c("VariantAnnotation", "preprocessCore")) { | ||
| if (!requireNamespace(pkg, quietly = TRUE)) { | ||
| stop("The splatPop simulation requires the ", pkg, " package.") | ||
| } | ||
| } | ||
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| params <- new("SplatPopParams") | ||
| params <- setParams(params, ...) | ||
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| return(params) | ||
| } | ||
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| #' @importFrom checkmate checkInt checkIntegerish checkNumber checkNumeric | ||
| #' checkFlag | ||
| setValidity("SplatPopParams", function(object) { | ||
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| v <- getParams(object, c(slotNames(object))) | ||
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| checks <- c(eqtl.n = checkNumber(v$eqtl.n, lower = 0), | ||
| eqtl.dist = checkInt(v$eqtl.dist, lower = 1), | ||
| eqtl.maf.min = checkNumber(v$eqtl.maf.min, lower = 0, | ||
| upper = 0.5), | ||
| eqtl.maf.max = checkNumber(v$eqtl.maf.max, lower = 0, | ||
| upper = 0.5), | ||
| eqtl.ES.shape = checkNumber(v$eqtl.ES.shape, lower = 0), | ||
| eqtl.ES.rate = checkNumber(v$eqtl.ES.rate, lower = 0), | ||
| eqtl.group.specific = checkNumber(v$eqtl.group.specific, | ||
| lower = 0, upper = 1), | ||
| pop.mean.shape = checkNumber(v$pop.mean.shape, lower = 0), | ||
| pop.mean.rate = checkNumber(v$pop.mean.rate, lower = 0), | ||
| pop.cv.bins = checkInt(v$pop.cv.bins, lower = 1), | ||
| pop.cv.param = checkDataFrame(v$pop.cv.param), | ||
| similarity.scale = checkNumber(v$similarity.scale, lower = 0)) | ||
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| if (all(checks == TRUE)) { | ||
| valid <- TRUE | ||
| } else { | ||
| valid <- checks[checks != TRUE] | ||
| valid <- paste(names(valid), valid, sep = ": ") | ||
| } | ||
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| return(valid) | ||
| }) | ||
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| #' @importFrom methods callNextMethod | ||
| setMethod("show", "SplatPopParams", function(object) { | ||
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| pp <- list("Population params:" = c("(mean.shape)" = "pop.mean.shape", | ||
| "(mean.rate)" = "pop.mean.rate", | ||
| "[similarity.scale]" = "similarity.scale", | ||
| "[cv.bins]" = "pop.cv.bins", | ||
| "(cv.params)" = "pop.cv.param"), | ||
| "eQTL params:" = c("[eqtl.n]" = "eqtl.n", | ||
| "[eqtl.dist]" = "eqtl.dist", | ||
| "[eqtl.maf.min]" = "eqtl.maf.min", | ||
| "[eqtl.maf.max]" = "eqtl.maf.max", | ||
| "[eqtl.group.specific]" = "eqtl.group.specific", | ||
| "(eqtl.ES.shape)" = "eqtl.ES.shape", | ||
| "(eqtl.ES.rate)" = "eqtl.ES.rate")) | ||
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| callNextMethod() | ||
| showPP(object, pp) | ||
| }) | ||
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| #' @rdname setParam | ||
| setMethod("setParam", "SplatPopParams", function(object, name, value) { | ||
| checkmate::assertString(name) | ||
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| # splatPopParam checks | ||
| if (name == "pop.cv.param") { | ||
| if (getParam(object, "pop.cv.bins") != nrow(value)) { | ||
| stop("Need to set pop.cv.bins to length of pop.cv.param") | ||
| } | ||
| } | ||
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| if (name == "eqtl.maf.min") { | ||
| if (getParam(object, "eqtl.maf.min") >= getParam(object, "eqtl.maf.max")) { | ||
| stop("Range of acceptable Minor Allele Frequencies is too small... | ||
| Be sure eqtl.maf.min < eqtl.maf.max.") | ||
| } | ||
| } | ||
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| object <- callNextMethod() | ||
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| return(object) | ||
| }) |
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