normalizeTissueAware {yarn} | R Documentation |
This function provides a wrapper to various normalization methods developed. Currently it only wraps qsmooth and quantile normalization returning a log-transformed normalized matrix. qsmooth is a normalization approach that normalizes samples in a condition aware manner.
normalizeTissueAware(obj, groups, normalizationMethod = c("qsmooth", "quantile"), ...)
obj |
ExpressionSet object |
groups |
Vector of labels for each sample or a column name of the phenoData slot for the ids to filter. Default is the column names |
normalizationMethod |
Choice of 'qsmooth' or 'quantile' |
... |
Options for |
ExpressionSet object with an assayData called normalizedMatrix
The function qsmooth comes from the qsmooth packages currently available on github under user 'kokrah'.
data(skin) normalizeTissueAware(skin,"SMTSD")