DESeq_nbinom:
Function to perform a DESeq analysis to detect differential expression
between perturbation and control groups.
Description
This function is a wrapper for a standard DESeq analyis
with two classes, perturbation and control, annotated in the
'conditions' column of the cds phenoData slot. First , the size factors
are determined using default parameters. Next, a dispersion parameter is
estimated using the default (pooled) method. Finally, p-values are
estimated for differential expression between treatment and control
groups.
A CountDataSet with perturbation and control
samples identified in the pData condition slot.
control
Character string corresponding to the control factor level of the
condition phenoData slot.
perturb
Character string corresponding to the perturbation factor level of the
condition phenoData slot.
try.hard
Logical parameter indicating the function's behavior in case the
parametric (default) dispersion estimation fails. If FALSE (default),
the function exits with an error. If TRUE, a non-parametric (loess)
esimation is attempted instead.
control_perturb_col
Column name in phenoData of
cds where control/perturbation designations are stored.