| calcNormFactors |
Calculate Normalization Factors to Align Columns of a Count Matrix |
| calcNormOffsetsforChIP |
Normalize ChIP-Seq Read Counts to Input and Test for Enrichment |
| camera.DGEList |
Competitive Gene Set Test for Digital Gene Expression Data Accounting for Inter-gene Correlation |
| commonCondLogLikDerDelta |
Conditional Log-Likelihoods in Terms of Delta |
| condLogLikDerDelta |
Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries |
| condLogLikDerSize |
Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries |
| cpm |
Counts per Million or Reads per Kilobase per Million |
| cpm.default |
Counts per Million or Reads per Kilobase per Million |
| cpm.DGEList |
Counts per Million or Reads per Kilobase per Million |
| cutWithMinN |
Cut numeric vector into non-empty intervals |
| decideTestsDGE |
Multiple Testing Across Genes and Contrasts |
| designAsFactor |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| deviances.function |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| DGEExact-class |
differential expression of Digital Gene Expression data - class |
| DGEGLM-class |
Digital Gene Expression Generalized Linear Model results - class |
| DGEList |
DGEList Constructor |
| DGEList-class |
Digital Gene Expression data - class |
| DGELRT-class |
Digital Gene Expression Likelihood Ratio Test data and results - class |
| dglmStdResid |
Visualize the mean-variance relationship in DGE data using standardized residuals |
| dim.DGEExact |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dim.DGEGLM |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dim.DGEList |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dim.DGELRT |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dim.TopTags |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| dimnames.DGEExact |
Retrieve the Dimension Names of a DGE Object |
| dimnames.DGEGLM |
Retrieve the Dimension Names of a DGE Object |
| dimnames.DGEList |
Retrieve the Dimension Names of a DGE Object |
| dimnames.DGELRT |
Retrieve the Dimension Names of a DGE Object |
| dimnames.TopTags |
Retrieve the Dimension Names of a DGE Object |
| dimnames<-.DGEGLM |
Retrieve the Dimension Names of a DGE Object |
| dimnames<-.DGEList |
Retrieve the Dimension Names of a DGE Object |
| dispBinTrend |
Estimate Dispersion Trend by Binning for NB GLMs |
| dispCoxReid |
Estimate Common Dispersion for Negative Binomial GLMs |
| dispCoxReidInterpolateTagwise |
Estimate Tagwise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile Likelihood |
| dispCoxReidPowerTrend |
Estimate Dispersion Trend for Negative Binomial GLMs |
| dispCoxReidSplineTrend |
Estimate Dispersion Trend for Negative Binomial GLMs |
| dispDeviance |
Estimate Common Dispersion for Negative Binomial GLMs |
| dispPearson |
Estimate Common Dispersion for Negative Binomial GLMs |
| getCounts |
Extract Specified Component of a DGEList Object |
| getDispersion |
Extract Specified Component of a DGEList Object |
| getDispersions |
Visualize the mean-variance relationship in DGE data using standardized residuals |
| getOffset |
Extract Specified Component of a DGEList Object |
| getPriorN |
Get a Recommended Value for Prior N from DGEList Object |
| glmFit |
Genewise Negative Binomial Generalized Linear Mdels |
| glmFit.default |
Genewise Negative Binomial Generalized Linear Mdels |
| glmFit.DGEList |
Genewise Negative Binomial Generalized Linear Mdels |
| glmLRT |
Genewise Negative Binomial Generalized Linear Mdels |
| glmQLFTest |
Genewise Negative Binomial Generalized Linear Mdels |
| gof |
Goodness of Fit Tests for Multiple GLM Fits |
| goodTuring |
Good-Turing Frequency Estimation |
| goodTuringPlot |
Good-Turing Frequency Estimation |
| goodTuringProportions |
Good-Turing Frequency Estimation |
| length.DGEExact |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| length.DGEGLM |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| length.DGEList |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| length.DGELRT |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| length.TopTags |
Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object |
| locfitByCol |
Locally Weighted Mean By Column |
| loessByCol |
Locally Weighted Mean By Column |
| maPlot |
Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data |
| maximizeInterpolant |
Maximize a function given a table of values by spline interpolation. |
| maximizeQuadratic |
Maximize a function given a table of values by quadratic interpolation. |
| mglm |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmLevenberg |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmLS |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmOneGroup |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmOneWay |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| mglmSimple |
Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors |
| movingAverageByCol |
Moving Average Smoother of Matrix Columns |
| mroast.DGEList |
Rotation Gene Set Tests for Digital Gene Expression Data |
| show-method |
differential expression of Digital Gene Expression data - class |
| show-method |
Digital Gene Expression Generalized Linear Model results - class |
| show-method |
Digital Gene Expression Likelihood Ratio Test data and results - class |
| show-method |
Table of the Top Differentially Expressed Tags |
| spliceVariants |
Identify Genes with Splice Variants |
| splitIntoGroups |
Split the Counts or Pseudocounts from a DGEList Object According To Group |
| splitIntoGroupsPseudo |
Split the Counts or Pseudocounts from a DGEList Object According To Group |
| subsetting |
Subset DGEList, DGEGLM, DGEExact and DGELRT Objects |
| systematicSubset |
Take a systematic subset of indices. |