XBSeq-package |
Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads |
Background |
Example Datasets used in the manual pages as well as in vignette |
conditions |
Accessor functions for the 'conditions' information in a XBSeqDataSet object. |
conditions-method |
Accessor functions for the 'conditions' information in a XBSeqDataSet object. |
conditions<--method |
Accessor functions for the 'conditions' information in a XBSeqDataSet object. |
counts |
Accessor functions for the 'counts' information in a XBSeqDataSet object. |
counts-method |
Accessor functions for the 'counts' information in a XBSeqDataSet object. |
dispEst |
Function to access the dispersion estimation for each gene |
dispEst-method |
Function to access the dispersion estimation for each gene |
dispEst<- |
Function to access the dispersion estimation for each gene |
dispEst<--method |
Function to access the dispersion estimation for each gene |
dispTable |
Access the dispersion table information for a XBSeqDataSet object |
dispTable-method |
Access the dispersion table information for a XBSeqDataSet object |
estimateRealCount |
Preliminary step to estimate the true signal based on observed signal and background noise |
estimateRealCount-method |
Preliminary step to estimate the true signal based on observed signal and background noise |
estimateSCV |
Estimate squared coefficient of variation for each gene |
estimateSCV-method |
Estimate squared coefficient of variation for each gene |
ExampleData |
Example Datasets used in the manual pages as well as in vignette |
fitInfo |
Accessor function for the fitInfo objects in a XBSeqDataSet |
fitInfo-method |
Accessor function for the fitInfo objects in a XBSeqDataSet |
genelength |
Example Datasets used in the manual pages as well as in vignette |
getSignalVars |
Estimate variance of the signal based on variance summation law |
MAplot |
Generate maplot after differential expression test |
Observed |
Example Datasets used in the manual pages as well as in vignette |
plotSCVEsts |
Plot estimated squared coefficient of variation |
scvBiasCorrectionFits |
Estimate squared coefficient of variation for each gene |
XBplot |
Examine the distribution of observed signal and background noise |
XBSeq |
Express function to carry out XBSeq analysis |
XBSeqDataSet |
Class '"XBSeqDataSet"' |
XBSeqDataSet-class |
Class '"XBSeqDataSet"' |
XBSeqTest |
XBSeq test for differential expression |