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" |
createDenovoGenome |
Create an annotatedGenome object that stores information about genes and transcripts |
denovoGeneExpr-class |
Class "denovoGeneExpr" |
denovoGenomeExpr-class |
Class "denovoGenomeExpr" |
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. |
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. |
mergeExp |
Merge splicing variant expression from multiple samples |
modelPrior |
Set prior distribution on expressed splicing variants. |
modelPriorAS-class |
Class "modelPriorAS" |
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" |
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 |
relativeExpr |
Estimate expression of gene splicing variants de novo. |
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" |
simMultSamples |
Simulate paired end reads for multiple samples based on pilot data |
simReads |
Function to simulate paired end reads following given read start and fragment length distributions and gene and variant expressions. |
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 "denovoGenomeExpr" |
[[-method |
Class "denovoGeneExpr" |