View source: R/core_mutSignatures_scr_5.R
1 | setMutClusterParams(num_processesToExtract = 2, num_totIterations = 10, num_parallelCores = 1, thresh_removeWeakMutTypes = 0.01, thresh_removeLastPercent = 0.07, distanceFunction = "cosine", num_totReplicates = 100, eps = 2.2204e-16, stopconv = 20000, niter = 1e+06, guided = TRUE, debug = FALSE, approach = "freq", stopRule = "DF", algorithm = "brunet", logIterations = "lite")
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num_processesToExtract |
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num_totIterations |
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num_parallelCores |
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thresh_removeWeakMutTypes |
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thresh_removeLastPercent |
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distanceFunction |
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num_totReplicates |
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eps |
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stopconv |
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niter |
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guided |
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debug |
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approach |
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stopRule |
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algorithm |
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logIterations |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 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 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
## The function is currently defined as
function (num_processesToExtract = 2, num_totIterations = 10,
num_parallelCores = 1, thresh_removeWeakMutTypes = 0.01,
thresh_removeLastPercent = 0.07, distanceFunction = "cosine",
num_totReplicates = 100, eps = 2.2204e-16, stopconv = 20000,
niter = 1e+06, guided = TRUE, debug = FALSE, approach = "freq",
stopRule = "DF", algorithm = "brunet", logIterations = "lite")
{
paramList <- list()
if (!((is.numeric(num_processesToExtract[1]) & num_processesToExtract[1] >
0)))
stop("Provide a reasonable number of signatures/processes to extract")
paramList$num_processesToExtract <- round(num_processesToExtract[1])
if (!(is.numeric(num_totIterations[1]) & num_totIterations[1] >
0))
stop("Provide a reasonable number of iterations to run (Bootstrapping)")
paramList$num_totIterations <- round(num_totIterations[1])
if (!(is.numeric(num_parallelCores[1]) & num_parallelCores[1] >
0))
stop("Provide a reasonable number of CPU cores to use for the analysis")
paramList$num_parallelCores <- round(num_parallelCores[1])
if (!(is.numeric(thresh_removeWeakMutTypes[1]) & thresh_removeWeakMutTypes[1] >=
0 & thresh_removeWeakMutTypes[1] < 1))
stop("Provide a reasonable (0.00-0.99) number of low-occurring mutation types to remove from the input before starting the analysis")
paramList$thresh_removeWeakMutTypes <- thresh_removeWeakMutTypes[1]
if (!(is.numeric(thresh_removeLastPercent[1]) & thresh_removeLastPercent[1] >=
0 & thresh_removeLastPercent[1] < 1))
stop("Provide a reasonable (0.00-0.99) number for filtering out poor iterations")
paramList$thresh_removeLastPercent <- thresh_removeLastPercent[1]
allowed.dist.methods <- c("Braun-Blanquet", "Chi-squared",
"correlation", "cosine", "Cramer", "Dice", "eDice", "eJaccard",
"Fager", "Faith", "Gower", "Hamman", "Jaccard", "Kulczynski1",
"Kulczynski2", "Michael", "Mountford", "Mozley", "Ochiai",
"Pearson", "Phi", "Phi-squared", "Russel", "simple matching",
"Simpson", "Stiles", "Tanimoto", "Tschuprow", "Yule",
"Yule2", "Bhjattacharyya", "Bray", "Canberra", "Chord",
"divergence", "Euclidean", "fJaccard", "Geodesic", "Hellinger",
"Kullback", "Levenshtein", "Mahalanobis", "Manhattan",
"Minkowski", "Podani", "Soergel", "supremum", "Wave",
"Whittaker")
if (!(is.character(distanceFunction[1]) & distanceFunction[1] %in%
allowed.dist.methods))
stop("Unknown method for calculating distances. For options, run: <<summary(proxy::pr_DB)>>")
paramList$distanceFunction <- distanceFunction[1]
if (!(is.numeric(num_totReplicates[1]) & num_totReplicates[1] >
99))
stop("Provide a reasonable number of replicates for stability evaluation of the results")
paramList$num_totReplicates <- round(num_totReplicates[1])
if (!(is.numeric(eps[1]) & eps[1] > 0 & eps[1] < 1e-04))
stop("Provide a reasonably small number (0 < n < 0.0001) for data overflow prevention")
paramList$eps <- eps[1]
if (!(is.numeric(stopconv[1]) & stopconv[1] >= 500))
stop("Provide a reasonable large number: number of 'conn-matrix-stable' iterations before stopping NMF")
paramList$stopconv <- round(stopconv[1])
if (!(is.numeric(niter[1]) & niter[1] >= 20000))
stop("Provide a reasonable large number: total NMF iterations")
paramList$niter <- round(niter[1])
paramList$guided <- ifelse(guided, TRUE, FALSE)
paramList$debug <- ifelse(debug, TRUE, FALSE)
paramList$approach <- ifelse(approach == "counts", "counts",
"freq")
paramList$stopRule <- ifelse(stopRule == "LA", "LA", "DF")
paramList$algorithm <- ifelse(tolower(algorithm) %in% c("brunet",
"alexa"), "brunet", "chihjen")
paramList$logIterations <- ifelse(tolower(logIterations) %in%
c("lite", "light", "li"), "lite", "full")
return(new(Class = "mutFrameworkParams", params = paramList))
}
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