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

View source: R/fileutilities.R

ct.buildSER Documentation

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))

RussBainer/gCrisprTools documentation built on Nov. 5, 2022, 2:35 p.m.