annotatedGenome |
Class "annotatedGenome" |
annotatedGenome-class |
Class "annotatedGenome" |
as.list-method |
Class "denovoGenomeExpr" |
calcDenovo |
Estimate expression of gene splicing variants de novo. |
calcExp |
Estimate expression of a known set of gene splicing variants. |
coef-method |
Class "modelPriorAS" |
coef-method |
Class "simulatedSamples" |
createDenovoGenome |
Create an annotatedGenome object that stores information about genes and transcripts |
denovoExpr |
Estimate expression for de novo splicing variants. |
denovoGeneExpr-class |
Class "denovoGeneExpr" |
denovoGenomeExpr-class |
Class "denovoGenomeExpr" |
exprs-method |
Class "simulatedSamples" |
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 |
hg19DB |
Subset of human genome (UCSC hg19 version) |
K562.r1l1 |
Toy RNA-seq data from RGASP project. |
lines |
Plot estimated read start and fragment length distributions. |
lines-method |
Plot estimated read start and fragment length distributions. |
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" |
names-method |
Class "denovoGeneExpr" |
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 |
Posterior probability that differences between group means are greater than a given threshold, i.e. that groups are non-equivalent by a biologically meaningful amount. |
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 |
quantileNorm |
Apply quantile normalization |
quantileNorm-method |
Apply quantile normalization |
relativeExpr |
Estimate expression of gene splicing variants de novo. |
relexprByGene |
Compute relative expressions within each gene |
rmShortInserts |
Remove reads with short insert sizes from imported BAM files. |
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" |
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. |
transcripts |
Returns all transcripts associated to a given island or entrez id stored in an annotatedGenome object. |
transcripts-method |
Returns all transcripts associated to a given island or entrez id stored in an annotatedGenome object. |
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' ~~ |
variants |
Class "denovoGeneExpr" |
variants-method |
Class "denovoGeneExpr" |
variants<- |
Class "denovoGeneExpr" |
variants<--method |
Class "denovoGeneExpr" |
wrapKnown |
Run all necessary steps to analyze a bam file with the casper pipeline. |
[-method |
Class "denovoGenomeExpr" |
[-method |
Class "denovoGeneExpr" |
[-method |
Class "modelPriorAS" |
[-method |
Class "simulatedSamples" |
[[-method |
Class "denovoGenomeExpr" |
[[-method |
Class "denovoGeneExpr" |