Characterization of Alternative Splicing based on Paired-End Reads


[Up] [Top]

Documentation for package ‘casper’ version 2.16.1

Help Pages

A C D E G H K L M N P Q R S T V W misc

-- A --

annotatedGenome Class "annotatedGenome"
annotatedGenome-class Class "annotatedGenome"
as.list-method Class "denovoGenomeExpr"
asymmetryCheck Plot asymmetry coefficients for the observed data and compare to those expected under Normality.
asymmetryCheck-method Plot asymmetry coefficients for the observed data and compare to those expected under Normality.

-- C --

calcDenovo Estimate expression of gene splicing variants de novo.
calcExp Estimate expression of a known set of gene splicing variants.
casperDesign Simulate paired end reads for multiple future samples based on pilot data, and obtain their expression estimates via casper
coef-method Class "modelPriorAS"
coef-method Class "simulatedSamples"
createDenovoGenome Create an annotatedGenome object that stores information about genes and transcripts

-- D --

denovoExpr Estimate expression for de novo splicing variants.
denovoGeneExpr-class Class "denovoGeneExpr"
denovoGenomeExpr-class Class "denovoGenomeExpr"
distrsGSE37704 Estimated read start and insert size distributions from MiSeq data in GEO dataset GSE37704.

-- E --

exprs-method Class "simulatedSamples"

-- G --

genePlot Plot exon structure for each transcript of a given gene.
genePlot-method Plot exon structure for each transcript of a given gene.
genePlot-methods Plot exon structure for each transcript of a given gene.
getChr 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.
getChr-method 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.
getDistrs Compute fragment start and fragment length distributions
getIsland 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.
getIsland-method 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.
getNreads Get total number of paths in each island from a pathCounts object.
getNreads-method Get total number of paths in each island from a pathCounts object.
getReads getReads returns the reads stored in a 'procBam' object.
getReads-method getReads returns the reads stored in a 'procBam' object.
getRoc Operating characteristics of differential expression analysis
getRoc-method Operating characteristics of differential expression analysis

-- H --

hg19DB Subset of human genome (UCSC hg19 version)

-- K --

K562.r1l1 Toy RNA-seq data from RGASP project.

-- L --

lines Plot estimated read start and fragment length distributions.
lines-method Plot estimated read start and fragment length distributions.

-- M --

matchTranscripts 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.
mergeBatches 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.
mergeBatches-method 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.
mergeExp Merge splicing variant expression from multiple samples
modelPrior Set prior distribution on expressed splicing variants.
modelPriorAS-class Class "modelPriorAS"

-- N --

names-method Class "denovoGeneExpr"

-- P --

pathCounts Compute exon path counts
pathCounts-class Class "pathCounts"
pathCounts-method Compute exon path counts
plot Plot estimated read start and fragment length distributions.
plot-method Plot estimated read start and fragment length distributions.
plotExpr Plot inferred gene structure and expression.
plotExpr-method Plot inferred gene structure and expression.
plotExpr-methods Plot inferred gene structure and expression.
plotPriorAS Plot prior distribution on set of expressed variants (i.e. the model space).
plotPriorAS-method Plot prior distribution on set of expressed variants (i.e. the model space).
plotPriorAS-methods Plot prior distribution on set of expressed variants (i.e. the model space).
posprob Class "denovoGeneExpr"
posprob-method Class "denovoGeneExpr"
probNonEquiv '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.
probNonEquiv-method '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.
procBam Process BAM object
procBam-class Class "procBam"
procBam-method Process BAM object
procGenome Create an annotatedGenome object that stores information about genes and transcripts
procGenome-method Create an annotatedGenome object that stores information about genes and transcripts
pvalTreat '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.
pvalTreat-method '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.

-- Q --

qqgammaGenomeWide Genome-wide qq-normal and qq-gamma plots
qqgammaGenomeWide-method Genome-wide qq-normal and qq-gamma plots
qqnormGenomeWide Genome-wide qq-normal and qq-gamma plots
qqnormGenomeWide-method Genome-wide qq-normal and qq-gamma plots
quantileNorm Apply quantile normalization
quantileNorm-method Apply quantile normalization

-- R --

relexprByGene Compute relative expressions within each gene
rmShortInserts Remove reads with short insert sizes from imported BAM files.

-- S --

show-method Class "annotatedGenome"
show-method Class "denovoGenomeExpr"
show-method Class "denovoGeneExpr"
show-method Class "modelPriorAS"
show-method Class "pathCounts"
show-method Class "procBam"
show-method Class "simulatedSamples"
simMAE Simulate Mean Absolute Error (MAE) in estimating isoform expression under various experimental settings.
simMAEcheck Model checking for One Sample Problems.
simMultSamples Simulate paired end reads for multiple future samples based on pilot data, and obtain their expression estimates via casper
simReads Function to simulate paired end reads following given read start and fragment length distributions and gene and variant expressions.
simulatedSamples-class Class "simulatedSamples"
splitGenomeByLength Split an annotatedGenome object into subsets according to gene length
subsetGenome subsetGenome subsets an object of class annotatedGenome for a set of island IDs or chromosome names.
subsetGenome-method subsetGenome subsets an object of class annotatedGenome for a set of island IDs or chromosome names.
subsetGenome-methods subsetGenome subsets an object of class annotatedGenome for a set of island IDs or chromosome names.

-- T --

transcripts 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.
transcripts-method 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.
txLength ~~ Methods for Function 'txLength' in Package 'casper' ~~
txLength-method ~~ Methods for Function 'txLength' in Package 'casper' ~~
txLength-methods ~~ Methods for Function 'txLength' in Package 'casper' ~~

-- V --

variants Class "denovoGeneExpr"
variants-method Class "denovoGeneExpr"
variants<- Class "denovoGeneExpr"
variants<--method Class "denovoGeneExpr"

-- W --

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

-- misc --

[-method Class "denovoGenomeExpr"
[-method Class "denovoGeneExpr"
[-method Class "modelPriorAS"
[-method Class "simulatedSamples"
[[-method Class "denovoGenomeExpr"
[[-method Class "denovoGeneExpr"