Does anyone else have this problem?
or else does anyone know what the function glmnb.fit is supposed to be?
I updated my statmod library, but I don't see the function.
Code:
library(DEXSeq) annotationfile = file.path("/TN_RNA-Seq/Alt_SPlicing/DEXSeq/hg19.prepared.gtf") samples=read.table("Targets/Samples.txt",row.names=1) inDir=file.path("/TN_RNA-Seq/Alt_SPlicing/DEXSeq/Targets") ecs = read.HTSeqCounts(countfiles = file.path(inDir, paste(rownames(samples))),design = samples,flattenedfile = annotationfile) ecs <- makeCompleteDEUAnalysis(ecs) Dispersion estimation. (Progress report: one dot per 100 genes) Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" In addition: Warning message: In .local(object, ...) : Exons with less than 11 counts will be discarded. For more details read the documentation, parameter minCount Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitted.values(glmnb.fit(mm, y, initialGuess, mf$offset, start = start)) : could not find function "glmnb.fit" Error in fitDispersionFunction(ecs) : no CR dispersion estimations found, please first call estimateDispersions function In addition: There were 22 warnings (use warnings() to see them)
I updated my statmod library, but I don't see the function.
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