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zeroWeightsLS() errors out if DESeq2 package isn't attached #4

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mjsteinbaugh opened this issue May 22, 2018 · 0 comments
Open

zeroWeightsLS() errors out if DESeq2 package isn't attached #4

mjsteinbaugh opened this issue May 22, 2018 · 0 comments

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@mjsteinbaugh
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mjsteinbaugh commented May 22, 2018

The zeroWeightsLS() function errors out if DESeq2 isn't attached because the package internally doesn't locate DESeqDataSetFromMatrix() in the namespace correctly:

> weights <- zingeR::zeroWeightsLS(
+     counts = counts,
+     design = design,
+     maxit = maxit,
+     normalization = "DESeq2_poscounts",
+     colData = colData,
+     designFormula = designFormula
+ )
converting counts to integer mode
Error in DESeqDataSetFromMatrix(counts$counts, colData = colData, design = designFormula) : 
  could not find function "DESeqDataSetFromMatrix"
> 
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