Man pages for Sage-Bionetworks/snm
Supervised Normalization of Microarrays
| buildBasisFunction | Builds Basis Fuction |
| buildBasisSplineMatrix | Build Basis Spline Matrix |
| calcArrayEffects | Calulate Array Effects Using Random Effects Model |
| calcSig | Performs inference on data. |
| calculate.nulls | Calculate the Identity of the Null Probes Identify Null... |
| checkArguments | Not very useful quite yet, but if software is expanded to... |
| constructNormalizedData | Construct Normalized Data |
| edge.fit | Fits Model to Data |
| edge.glr | Calculate Test Statistics and P values |
| edge.qvalue | Qvalue function from EDGE software |
| err.msg | Error Message |
| fit.fast.model | Fast Version of SNM Algorithm |
| fit.model | Builds and Fits the Mixed Effects Model Fit Random Effects... |
| fit.pset | Summarize probe-level data into probe sets |
| fitted.snm | Extract fitted values from an snm object |
| f.pvalue | Calculates P values by fitting a full and reduced model to... |
| get.coefs | Estimate Coefficients Gets Coefficients From a Fitted Model |
| get.resids | Estimate Residuals |
| getSpanningSet | Split Data into Bins |
| makeDataObject | Makes data object for fitting the random effects model |
| make.ref.model.matrices | Make Model Matrices for Random Effects Model |
| make.snm.obj | Make Snm Object |
| plot.snm | Display plots for an snm object |
| rm.zero.cols | Cleans Model Matrices |
| sim.doubleChannel | Simulated data for a double channel microarray experiment. |
| sim.function.var | Function simulates data as a function of a variable |
| sim.intensity.dep | Simulate Intensity Dependent Variables |
| sim.preProcessed | Simulate data from a microarray experiment without any... |
| sim.probe.specific | Simulate a Probe-Specific Variable |
| sim.refDesign | Simulates data from a two-color microarray experiment using a... |
| sim.singleChannel | Simulate data from a single channel microarray experiment |
| snm | Perform a supervised normalization of microarray data |
| snm.diagnosticPlot | Produce Diagnostic Plots For SNM Algorithm |
| snm-internal | Internal snm functions. |
| summary.snm | Display summary information for an snm object |
| sva | Estimate surrogate variables with an iterative algorithm from... |
