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casper (version 2.6.0)

Characterization of Alternative Splicing based on Paired-End Reads

Description

Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

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Version

Version

2.6.0

License

GPL (>=2)

Maintainer

David Rossell

Last Published

February 15th, 2017

Functions in casper (2.6.0)

denovoGeneExpr-class

Class "denovoGeneExpr"

Estimate expression of gene splicing variants de novo.

splitGenomeByLength

Split an annotatedGenome object into subsets according to gene length

Set prior distribution on expressed splicing variants.

Merge two ExpressionSet objects by doing quantile normalization and computing partial residuals (i.e. substracting group mean expression in each batch). As currently implemented the method is only valid for balanced designs, e.g. each batch has the same number of samples per group.

Plot asymmetry coefficients for the observed data and compare to those expected under Normality.

Operating characteristics of differential expression analysis

subsetGenome subsets an object of class annotatedGenome for a set of island IDs or chromosome names.

denovoGenomeExpr-class

Class "denovoGenomeExpr"

Get total number of paths in each island from a pathCounts object.

Model checking for One Sample Problems.

Estimate expression for de novo splicing variants.

Run all necessary steps to get expression estimates from multiple bam files with the casper pipeline.

Plot prior distribution on set of expressed variants (i.e. the model space).

annotatedGenome-class

Class "annotatedGenome"

probNonEquiv performs a Bayesian hypothesis test for equivalence between group means. It returns the posterior probability that |mu1-mu2|>logfc. pvalTreat is a wrapper to treat in package limma, which returns P-values for the same hypothesis test.

Process BAM object

Subset of human genome (UCSC hg19 version)

~~ Methods for Function txLength in Package casper ~~

Simulate Mean Absolute Error (MAE) in estimating isoform expression under various experimental settings.

Extracts transcript information (exon start and ends) from an annotatedGenome object, either for all transcripts or only those corresponding to a given island or transcript.

Merge splicing variant expression from multiple samples

getIsland returns the island id associated to a given entrez or transcript id in an annotatedGenome object. getChr indicates the chromosome for a given Entrez, transcript or island id.

Compute relative expressions within each gene

Compute fragment start and fragment length distributions

Compute exon path counts

qqnormGenomeWide

Genome-wide qq-normal and qq-gamma plots

pathCounts-class

Class "pathCounts"

Plot estimated read start and fragment length distributions.

Class "procBam"

modelPriorAS-class

Class "modelPriorAS"

Plot exon structure for each transcript of a given gene.

Function to simulate paired end reads following given read start and fragment length distributions and gene and variant expressions.

Run all necessary steps to get expression estimates from multiple bam files with the casper pipeline.

Estimated read start and insert size distributions from MiSeq data in GEO dataset GSE37704.

Plot inferred gene structure and expression.

Create an annotatedGenome object that stores information about genes and transcripts

Remove reads with short insert sizes from imported BAM files.

Toy RNA-seq data from RGASP project.

getReads returns the reads stored in a procBam object.

Estimate expression of a known set of gene splicing variants.

Simulate paired end reads for multiple future samples based on pilot data, and obtain their expression estimates via casper

simulatedSamples-class

Class "simulatedSamples"

Apply quantile normalization