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...
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@@ -59,7 +59,7 @@ distributedCogaps <- function(data, allParams, uncertainty)
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59
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allParams$BPPARAM <- BiocParallel::MulticoreParam(workers=length(sets))
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60
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60
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initialResult <- NULL
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62
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- if (is.null(allParams$fixedPatterns))
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+ if (is.null(allParams$gaps@fixedPatterns))
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{
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# run Cogaps normally on each subset of the data
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gapsCat(allParams, "Running Across Subsets...\n\n")
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...
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...
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@@ -80,13 +80,13 @@ distributedCogaps <- function(data, allParams, uncertainty)
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}
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else
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{
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83
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- matchedPatterns <- list(consensus=allParams$fixedPatterns)
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+ matchedPatterns <- list(consensus=allParams$gaps@fixedPatterns)
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}
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85
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# set fixed matrix
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allParams$gaps@nPatterns <- ncol(matchedPatterns$consensus)
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88
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- allParams$fixedPatterns <- matchedPatterns$consensus
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89
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- allParams$whichMatrixFixed <- ifelse(allParams$gaps@distributed
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+ allParams$gaps@fixedPatterns <- matchedPatterns$consensus
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+ allParams$gaps@whichMatrixFixed <- ifelse(allParams$gaps@distributed
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== "genome-wide", "P", "A")
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91
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# run final phase with fixed matrix
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