Arguments
expressionValues
A numeric vector that indicates expression levels. This is the only required parameter.
lengths
An integer vector that indicates the length of the genomic region that corresponds to each expression value. The order of these values must be identical to the order of the expression values. This parameter is optional.
gcContent
A numeric vector that indicates the proportion of bases in the genomic region that are a G or C nucleotide. The order of these values must be identical to the order of the expression values. This parameter is optional.
modelType
Various models can be used for the mixture model to differentiate between active and inactive probes. The default is the normal-normal model (``nn''), which uses the normal distribution. Other available options are log-normal (``ln''), negative-binomial (``nb''), and normal-normal Bayes (``nn_bayes'').
convThreshold
Convergence threshold that determines at what point the mixture-model parameters have stabilized. The default value should be suitable in most cases. However, if the model fails to converge (or converges too quickly), it may be useful to adjust this value. Optional.
higherValuesIndicateHigherExpression
In most cases, higher expression values indicate relatively high expression. However, if higher values indicate relatively low expresssion, this parameter can be used to indicate such. Accordingly, UPC values closer to one will indicate higher expression, and UPC values closer to zero will indicate the opposite. Optional.
verbose
Whether to output more detailed status information as processing occurs. Default is TRUE.