Function to perform a DESeq analysis to detect differential expression between perturbation and control groups.

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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.

Usage

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.DESeq_nbinom(cds, control = "control", perturb = "perturbation",
try.hard = FALSE, control_perturb_col = "cmap",...)

Arguments

cds

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.

...

Any additional parameters passed on to estimateDispersions

Value

See nbinomTest for details.

Note

To use this function, please install the suggested Bioconductor package 'DESeq'.

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