makeExampleDESeqDataSet_multifac | R Documentation |
Constructs a simulated dataset of Negative Binomial data from different conditions.
The fold changes between the conditions can be adjusted with the betaSD_condition
and the betaSD_tissue
arguments.
makeExampleDESeqDataSet_multifac(
n = 1000,
m = 12,
betaSD_condition = 1,
betaSD_tissue = 3,
interceptMean = 4,
interceptSD = 2,
dispMeanRel = function(x) 4/x + 0.1,
sizeFactors = rep(1, m)
)
n |
number of rows (genes) |
m |
number of columns (samples) |
betaSD_condition |
the standard deviation for condition betas, i.e. beta ~ N(0,betaSD) |
betaSD_tissue |
the standard deviation for tissue betas, i.e. beta ~ N(0,betaSD) |
interceptMean |
the mean of the intercept betas (log2 scale) |
interceptSD |
the standard deviation of the intercept betas (log2 scale) |
dispMeanRel |
a function specifying the relationship of the dispersions on
|
sizeFactors |
multiplicative factors for each sample |
This function is designed and inspired following the proposal of
makeExampleDESeqDataSet
from the DESeq2
package. Credits are given
to Mike Love for the nice initial implementation
a DESeqDataSet
with true dispersion,
intercept for two factors (condition and tissue) and beta values in the
metadata columns. Note that the true betas are provided on the log2 scale.
dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
dds
dds2 <- makeExampleDESeqDataSet_multifac(betaSD_condition = 1, betaSD_tissue = 4)
dds2
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