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@@ -26,13 +26,13 @@ setMethod("MRihw", signature = "fitFeatureModelResults", function(obj, p, adjust
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# set covariate to be num of non-zero elements per row
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p <- obj@pvalues
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covariate <- rowSums(obj@counts != 0)
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- ihwRes <- ihw(p, covariate, alpha)
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+ ihwRes <- IHW::ihw(p, covariate, alpha)
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padj <- ihwRes@df$adj_pvalue
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}
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if (adjustMethod == "ihw-abundance"){
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# use feature median count as covariate
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covariate <- rowMedians(obj@counts)
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- ihwRes <- ihw(p, covariate, alpha)
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+ ihwRes <- IHW::ihw(p, covariate, alpha)
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padj <- ihwRes@df$adj_pvalue
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}
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padj
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@@ -61,7 +61,7 @@ setMethod("MRihw", signature = "fitZigResults", function(obj, p, adjustMethod, a
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if (adjustMethod == "ihw-abundance"){
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# use Amean as covariate
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covariate <- obj@eb$Amean
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- ihwRes <- ihw(p, covariate, alpha)
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+ ihwRes <- IHW::ihw(p, covariate, alpha)
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padj <- ihwRes@df$adj_pvalue
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}
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padj
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