Newer
Older
#' @export
newLunParams <- function(...) {
params <- new("LunParams")
params <- setParams(params, ...)
return(params)
}
#' @importFrom checkmate checkInt checkIntegerish checkNumber checkNumeric
object <- expandParams(object)
v <- getParams(object, slotNames(object))
nGroups <- v$nGroups
checks <- c(nGenes = checkInt(v$nGenes, lower = 1),
nCells = checkInt(v$nCells, lower = 1),
nGroups = checkInt(v$nGroups, lower = 1),
groupCells = checkIntegerish(v$groupCells, lower = 1,
len = nGroups),
mean.rate = checkNumber(v$mean.rate, lower = 0),
mean.shape = checkNumber(v$mean.shape, lower = 0),
count.disp = checkNumber(v$count.disp, lower = 0),
de.nGenes = checkIntegerish(v$de.nGenes, lower = 0,
len = nGroups),
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
len = nGroups),
de.upFC = checkNumeric(v$de.upFC, lower = 0,
len = nGroups),
de.downFC = checkNumeric(v$de.downFC, lower = 0,
len = nGroups),
seed = checkInt(v$seed, lower = 0))
# Check groupCells matches nCells, nGroups
if (v$nCells != sum(v$groupCells) || nGroups != length(v$groupCells)) {
checks <- c(checks,
"nCells, nGroups and groupCells are not consistent")
}
if (all(checks == TRUE)) {
valid <- TRUE
} else {
valid <- checks[checks != TRUE]
valid <- paste(names(valid), valid, sep = ": ")
}
return(valid)
})
#' @rdname setParam
setMethod("setParam", "LunParams", function(object, name, value) {
checkmate::assertString(name)
if (name == "nCells" || name == "nGroups") {
stop(name, " cannot be set directly, set groupCells instead")
}
if (name == "groupCells") {
object <- setParamUnchecked(object, "nCells", sum(value))
object <- setParamUnchecked(object, "nGroups", length(value))
}
object <- callNextMethod()
return(object)
})
setMethod("show", "LunParams", function(object) {
pp <- list("Groups:" = c("[Groups]" = "nGroups",
"[Group Cells]" = "groupCells"),
"Diff expr:" = c("[Genes]" = "de.nGenes",
"[Up Prop]" = "de.upProp",
"[Up FC]" = "de.upFC",
"[Down FC]" = "de.downFC"))
callNextMethod()
showPP(object, pp)
})
#' @rdname expandParams
setMethod("expandParams", "LunParams", function(object) {
n <- getParam(object, "nGroups")
vectors <- c("de.nGenes", "de.upProp", "de.upFC", "de.downFC")
object <- callNextMethod(object, vectors, n)
return(object)
})