Man pages for cn.farms
cn.FARMS - factor analysis for copy number estimation
| callSummarize | Defines which variables should be written back when calling a... |
| cn.farms | cn.farms |
| cnLibrary | This function was taken from snowfall and edited due to some... |
| combineData | Combine two ExpressionSet objects |
| createAnnotation | Creation of annotation files |
| createMatrix | Creates the needed matrix |
| distributionDistance | Computes the distribution distance |
| dnaCopySf | Runs DNAcopy in parallel mode |
| doCnFarmsSingle | Does the whole cn.farms process in one call |
| flcSnp6Std | Does a fragment length correction on intensities |
| flcStd | Does a fragment length correction on intensities |
| fragLengCorr | Does a fragment length correction |
| getFragmentSet | Finds SNPs which belong to one fragment |
| getSingleProbeSetSize | Combines data for probeset summarization |
| mlSummarization | Method for computation of the multi-loci summarization |
| normAdd | Extracts info from the package name |
| normalizeAverage | Scales the range of the non-polymorphic data to the range of... |
| normalizeCels | Wrapper for the normalization functions |
| normalizeNone | Runs the SOR normalization on microarray data |
| normalizeNpData | Processes the non-polymorphic data |
| normalizeQuantiles | Normalization Quantiles |
| normalizeSequenceEffect | Correction for probe sequence effects |
| normalizeSor | Runs the SOR normalization on microarray data |
| plotDendrogram | Plots a dendrogram |
| plotDensity | Function to create a density plot |
| plotEvalIc | Creates a plot with known regions and a numeric vector |
| plotRegions | Plots given regions by segments |
| plotSmoothScatter | Creates a smooth scatter plot |
| plotViolines | Create a violine plot |
| slSummarization | Method for computation of the single-locus summarization |
| sparseFarmsC | Normalizes the data with SOR |
| summarizeFarmsExact | Summarization Laplacian approach with exact computation |
| summarizeFarmsExact2 | Summarization Laplacian approach with exact computation |
| summarizeFarmsExact3 | Summarization Laplacian approach with exact computation |
| summarizeFarmsGaussian | Summarization Gaussian approach |
| summarizeFarmsMethods | Lists methods for possible FARMS summarization |
| summarizeFarmsStatistics | Mean or median instead of the FARMS model |
| summarizeFarmsVariational | Summarization variational Laplacian approach |
| summarizeWindowBps | Combines neighbouring locations to windows |
| summarizeWindowMethods | Lists methods for possible window methods |
| summarizeWindowStd | Combines neighbouring locations to windows |
