getSmoothedRTNormalizedMatrix {NormalyzerDE} | R Documentation |
Uses the function getRTNormalizedMatrix to generate multiple normalized matrices which are shifted respective to each other and finally merged into a single matrix. This could potentially reduce effect of fluctuations within individual windows.
getSmoothedRTNormalizedMatrix(rawMatrix, retentionTimes, normMethod, stepSizeMinutes, windowShifts = 2, windowMinCount = 100, mergeMethod = "mean", noLogTransform = FALSE)
rawMatrix |
Target matrix to be normalized |
retentionTimes |
Vector of retention times corresponding to rawMatrix |
normMethod |
The normalization method to apply to the time windows |
stepSizeMinutes |
Size of windows to be normalized |
windowShifts |
Number of frame shifts. |
windowMinCount |
Minimum number of features within window. |
mergeMethod |
Layer merging approach. Mean or median. |
noLogTransform |
Don't log transform the input |
Normalized matrix
data(example_data_small) data(example_data_only_values) data(example_design_small) retentionTimes <- as.numeric(example_data[, "Average.RT"]) dataMat <- example_data_only_values performCyclicLoessNormalization <- function(rawMatrix) { log2Matrix <- log2(rawMatrix) normMatrix <- limma::normalizeCyclicLoess(log2Matrix, method="fast") colnames(normMatrix) <- colnames(rawMatrix) normMatrix } rtNormMat <- getSmoothedRTNormalizedMatrix(dataMat, retentionTimes, performCyclicLoessNormalization, stepSizeMinutes=1, windowMinCount=100, windowShifts=2, mergeMethod="median")