An example of count data for an experiment without spike-ins
pulseRFractionData
A list containing simulated data, model and parameter information.
formulas describe the model for mean read number
counts contain the simulated data
conditions is a data.frame describing sample time point and type
fractions is a character vector to divide samples into groups for
normalisation
formulaIndexes is a list of formula names (see formulas), which are
used in linear combination with coefficients in normFactors to calculate
mean read number
normFactors are coefficients which relate quantities of RNA between
different groups and can be used as normalisation coefficients for
calculation of mean read numbers using formulas and formulaIndexes
par is a list of model parameters
The data set contains simulation of an experiment which measures three
fractions, namely, coded as 'A_fraction', 'B_fraction' and 'C_fraction'.
There are three types of quantities, 'A', 'B' and 'C' for which a kinetic
model is defined, see formulas element in the data set:
(A = a * p, B = a * b^time, C = a * (1 - b^time)),
where a, b are gene-specific parameters which are unknown, p is a vector of known gene-specific parameters (e.g. probability of capture depending on the uridine content etc.)
The data are generated for 3 replicates, 3 different time points and for
10 different genes, see elements counts and conditions.
The model considers possibility of cross-contamination with different types
of RNA, which is described by formulaIndexes. In this case,
the mean read number for a gene is a linear combination of the described
RNA types with weights defined in normFactors.
Due to different amounts of RNA in different conditions, the normalisation
factors are defined for groups of the samples, hence they are shared values
for a given sample group. The grouping is defined by groups element of the
data set.
The true parameter values, which are used for data simulation are in
par element. This also includes the size parameter for the negative
binomial distribution.