Calculate the expression of each bin in a BinnedFlowSample in terms of the measurement markers

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Description

getBinExpr main function definition

Arguments

method

Method to use to compute expression, passed as a string. Defaults to medianFI, which takes the simple median of each bin, and does not require control tubes. Other options available are medianFIDist, which uses medians with the median of the negative control subtracted out, and propPos which sets a threshold at the 98th percentile of the negative control and determines what proportion of cells lie above that.

include.bin.medians

logical, specifies whether to compute the medians of each bin in terms of the binning markers and include them in the result or not. Defaults to T.

scale

logical specifying whether to scale the results to the interval (0,1). If T (default), then all medians will be divided by the range for that marker as specified in the flowFrame.

Value

A numeric matrix containing expression values, with bins as rows and markers as columns

Examples

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data(amlsample)
normed.sample <- quantileNormalise(aml.sample)
binned.sample <- flowFPBin(normed.sample)
binned.sample <- removeSparseBins(binned.sample, 0.001)
bin.expr <- getBinExpr(binned.sample)
heatmap(bin.expr, scale='none')