ct.buildSE: Package Screen Data into a 'SummarizedExperiment' Object

In OscarBrock/gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Package Screen Data into a 'SummarizedExperiment' Object

Description

Convenience function to package major components of a screen into a 'SummarizedExperiment' container for downstream visualization and analysis. All arguments are optional except for 'es'.

Usage

ct.buildSE(
  es,
  sampleKey = NULL,
  ann = NULL,
  vm = NULL,
  fit = NULL,
  summaryList = NULL
)

Arguments

es	An 'ExpressionSet' of screen data. Required.
sampleKey	a gCrisprTools 'sampleKey' object, to be added to the 'colData'.
ann	Annotation object to be packaged into the 'rowData'
vm	A 'voom'-derived normalized object
fit	a 'MArrayLM' object containing the contrast information and model results
summaryList	A named list of data.frames, returned by ct.generateResults. if you need to generate one of these by hand for some reason, see the example resultsDF object loaded in the example below.

Value

A 'SummarizedExperiment' object.

Author(s)

Russell Bainer

Examples

data('ann', 'es', 'fit', 'resultsDF')
ct.buildSE(es, ann = ann, fit = 'fit', summaryList = list('resA' = resultsDF, 'resB' = resultsDF))

OscarBrock/gCrisprTools documentation built on Oct. 25, 2022, 7:29 a.m.