runLimmaPipeline: This function orchestrates imputation, normalization and the...
In MassDynamics/MassExpression: MassExpression
View source: R/runLimmaPipeline.R
runLimmaPipeline R Documentation
This function orchestrates imputation, normalization and the binary limma statistics accross all experimental comparisons
Description
This function orchestrates imputation, normalization and the binary limma statistics accross all experimental comparisons
Usage
runLimmaPipeline(
IntensityExperiment,
normalisationMethod,
fitSeparateModels,
returnDecideTestColumn,
conditionSeparator
)
Arguments
IntensityExperiment
Output from createSummarizedExperiment
normalisationMethod
logical. Whether to perform median normalisation by condition.
fitSeparateModels
logical. TRUE to fit separate limma models for each pairwise comparisons
(e.g. filtering and 'lmFit' are run separately by comparison).
returnDecideTestColumn
logical. If TRUE the row data of the 'CompleteIntensityExperiment' will contain the output from
'limma::decideTests'. If FALSE a single model is run for all contrasts.
conditionSeparator
string. String used to separate up and down condition in output.
MassDynamics/MassExpression documentation built on May 7, 2023, 11:29 a.m.
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View source: R/runLimmaPipeline.R
| runLimmaPipeline | R Documentation |
This function orchestrates imputation, normalization and the binary limma statistics accross all experimental comparisons
Description
This function orchestrates imputation, normalization and the binary limma statistics accross all experimental comparisons
Usage
runLimmaPipeline(
IntensityExperiment,
normalisationMethod,
fitSeparateModels,
returnDecideTestColumn,
conditionSeparator
)
Arguments
IntensityExperiment |
Output from createSummarizedExperiment |
normalisationMethod |
logical. Whether to perform median normalisation by condition. |
fitSeparateModels |
logical. TRUE to fit separate limma models for each pairwise comparisons (e.g. filtering and 'lmFit' are run separately by comparison). |
returnDecideTestColumn |
logical. If TRUE the row data of the 'CompleteIntensityExperiment' will contain the output from 'limma::decideTests'. If FALSE a single model is run for all contrasts. |
conditionSeparator |
string. String used to separate up and down condition in output. |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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