Man pages for blima
Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
| aggregateAndPreprocess | Aggregate data |
| bacgroundCorrect | Data background correction. |
| bacgroundCorrectSingleArray | Data background correction. |
| backgroundChannelSubtract | Background channel subtraction |
| backgroundChannelSubtractSingleArray | Background channel subtraction |
| blima-package | Package for the preprocessing and analysis of the Illumina... |
| channelExistsIntegrityWithLogicalVectorList | Internal function |
| checkIntegrity | Internal function |
| checkIntegrityLogical | Internal function |
| checkIntegrityOfListOfBeadLevelDataObjects | Internal function |
| checkIntegrityOfSingleBeadLevelDataObject | Internal function |
| chipArrayStatistics | Statistics of beadLevelData |
| createSummarizedMatrix | Summarized value matrix. |
| doAction | Internal function |
| doProbeTTests | T-test for probe level data. |
| doTTests | T-test for bead (detector) level data. |
| filterBg | Bg correct vector |
| getNextVector | Support probe and beadl level testing. |
| initMeanDistribution | initMeanDistribution |
| insertColumn | Internal function to support chipArrayStatistics |
| interpolateSortedVector | Interpolate sorted vector |
| interpolateSortedVectorRcpp_ | interpolateSortedVectorRcpp |
| log2TransformPositive | Log2 transform of numbers >1. |
| meanDistribution | Produce sorted double vector with mean distribution. |
| nonParametricEstimator | INTERNAL FUNCTION Xie background correct. |
| nonPositiveCorrect | Correct non positive |
| nonPositiveCorrectSingleArray | Correct non positive |
| numberOfDistributionElements | Internal |
| performXieCorrection | INTERNAL FUNCTION Xie background correct. |
| plotBackgroundImageAfterCorrection | Plot background image after correction |
| plotBackgroundImageBeforeCorrection | Plot background image before correction |
| quantileNormalize | Bead level quantile normalization. |
| readToVector | Support doTTests function. |
| selectedChannelTransform | Channel transformation |
| selectedChannelTransformSingleArray | Channel transformation |
| singleArrayNormalize | Bead level quantile normalization. |
| singleChannelExistsIntegrityWithLogicalVector | Internal function |
| singleCheckIntegrityLogicalVector | Internal function |
| singleNumberOfDistributionElements | Internal |
| updateMeanDistribution | updateMeanDistribution |
| varianceBeadStabilise | Bead level VST. |
| varianceBeadStabiliseSingleArray | Bead level VST. |
| vstFromLumi | Function from LGPL lumi package 2.16.0 |
| writeBackgroundImages | Write Background Images |
| xieBacgroundCorrect | Xie background correct. |
| xieBacgroundCorrectSingleArray | INTERNAL FUNCTION Xie background correct. |
