normMethods {NormalyzerDE} | R Documentation |
Perform normalizations on Normalyzer dataset
normMethods( nds, forceAll = FALSE, normalizeRetentionTime = TRUE, quiet = FALSE, rtStepSizeMinutes = 1, rtWindowMinCount = 100, rtWindowShifts = 1, rtWindowMergeMethod = "mean", noLogTransform = FALSE )
nds |
Normalyzer dataset object. |
forceAll |
Force all methods to run despite not qualifying for thresholds. |
normalizeRetentionTime |
Perform retention time based normalization methods. |
quiet |
Prevent diagnostic output |
rtStepSizeMinutes |
Retention time normalization window size. |
rtWindowMinCount |
Minimum number of datapoints in each retention-time segment. |
rtWindowShifts |
Number of layered retention time normalized windows. |
rtWindowMergeMethod |
Merge approach for layered retention time windows. |
noLogTransform |
Per default NormalyzerDE performs a log-transformation on the input data. If not needed, specify this option |
Returns Normalyzer results object with performed analyzes assigned as attributes
data(example_summarized_experiment) normObj <- getVerifiedNormalyzerObject("job_name", example_summarized_experiment) normResults <- normMethods(normObj)