alpine (version 0.99.1)

preprocessedData: Preprocessed data for vignettes and examples

Description

The following data objects are prepared for use in the alpine vignette and examples pages, as the preparation of these objects requires either long running time or a large amount of disk space.

Format

ebt.fit and ebt.theta are GRangesList. fitpar, fitpar.small, res are lists created by alpine functions. genes.theta is a character vector. txdf.theta is a DataFrame.

Source

See vignette for details of object construction. The alignments come from alpineData (4 samples from GEUVADIS project), the Ensembl gene annotations come from Homo_sapiens.GRCh38.84.gtf, and the genome is BSgenome.Hsapiens.NCBI.GRCh38.

Details

• ebt.fit - the GRangesList prepared in the vignette for fitting the bias models
• fitpar - the fitted parameters, similar to those made in the vignette, but using minsize=80 and maxsize=350
• fitpar.small - the fitted parameters from the vignette, returned by fitBiasModels
• res - the results object from the vignette, returned by estimateTheta
• ebt.theta - the GRangesList prepared in the vignette for running estimateTheta
• genes.theta - the names of genes used in the vignette for running estimateTheta
• txdf.theta - the DataFrame of gene and transcript information used in the vignette for running estimateTheta