Usage
UPC_RNASeq_Single(expressionValues, featureNames, lengths = NULL, gcContent = NULL, modelType = "nn", convThreshold = 0.01, ignoreZeroes = FALSE, verbose = TRUE)
Arguments
expressionValues
A vector of RNA-Seq count values. Required.
featureNames
A vector of unique names that correspond to the count values. Required.
lengths
A vector indicating the length (in genomic bases) of the genomic region that corresponds to the count values.
gcContent
A vector indicating the number of G/C bases in the genomic region that corresponds to the count values.
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. (This parameter is optional.)
ignoreZeroes
Whether to ignore read counts equal to zero when performing UPC calculations. Default is FALSE.
verbose
Whether to output more detailed status information as files are normalized. Default is TRUE.