makeExampleDESeqDataSet_multifac {pcaExplorer} | 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