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 |
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. |
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. |