alpine


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Documentation for package ‘alpine’ version 1.0.0

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alpine-package alpine: bias corrected transcript abundance estimation
buildFragtypes Build fragment types from exons
ebt.fit Preprocessed data for vignettes and examples
ebt.theta Preprocessed data for vignettes and examples
estimateAbundance Estimate bias-corrected transcript abundances (FPKM)
extractAlpine Extract results from estimateAbundance run across genes
fitBiasModels Fit bias models over single-isoform genes
fitpar Preprocessed data for vignettes and examples
fitpar.small Preprocessed data for vignettes and examples
genes.theta Preprocessed data for vignettes and examples
getFragmentWidths Get fragment widths
getReadLength Get read length
mergeGenes Merge overlapping "genes" into gene clusters
normalizeDESeq DESeq median ratio normalization for matrix
plotFragLen Plot fragment length distribution over samples
plotGC Plot the fragment GC bias over samples
plotGRL Simple segments plot for GRangesList
plotOrder0 Plot parameters of the variable length Markov model (VLMM) for read starts
plotOrder1 Plot parameters of the variable length Markov model (VLMM) for read starts
plotOrder2 Plot parameters of the variable length Markov model (VLMM) for read starts
plotRelPos Plot relative position bias over samples
predictCoverage Predict coverage for a single-isoform gene
preprocessedData Preprocessed data for vignettes and examples
res Preprocessed data for vignettes and examples
splitGenesAcrossChroms Split genes that have isoforms across chromosomes
splitLongGenes Split very long genes
txdf.theta Preprocessed data for vignettes and examples