Arguments
cds
CountDataSet with all count data
for a single instance, plus metadata on which samples are perturbation
and control.
vst
Matrix of variance-stabilized count data that must include
columns with colnames matching the sampleNames of the cds object. The
vst matrix may contain additional columns / samples, which will be ignored.
control_perturb_col
Column name in phenoData
of
cds
where control/perturbation designations are stored.
control
String designating control samples in the
control_perturb_col
column.
perturb
String designating perturbation samples in the
control_perturb_col
column.
try.hard
Logical parameter indicating how to proceed when
DESeq's parametric estimation of the dispersion parameter
fails. If set to FALSE (default), the function exits with an
error. If set to TRUE, the function will try a non-parametric
approach instead.