discoDFtoSE: Data formatting for DiscoRhythm

In matthewcarlucci/DiscoRhythm: Interactive Workflow for Discovering Rhythmicity in Biological Data

Data formatting for DiscoRhythm

Description

Functions to import a data.frame (from the format expected by the web application discoApp()) as a SummarizedExperiment object or to export a SummarizedExperiment for use with the web application.

Usage

discoDFtoSE(Maindata, Metadata = NULL, shinySession = NULL)

discoSEtoDF(se)

Arguments

Maindata	data.frame with the first column containing row IDs and all subsequent columns containing experimental values. Columns should follow the expected naming format described in the vignette.
Metadata	data.frame of sample data, usually generated by using discoParseMeta on the column names of the Maindata data.frame. If is.null(Metadata) and Maindata is provided as input, Metadata will be generated from Maindata.
shinySession	shiny session object for use only by the DiscoRhythm shiny app discoApp() to update the axis labels using the time value prefix.
se	SummarizedExperiment, the main data object used by DiscoRhythm expected to contain se$ID, se$ReplicateID, se$Time sample metadata and non-null rownames. See the vignette for more details.

Value

discoDFtoSE returns a SummarizedExperiment object with colData containing sample metadata.

discoSEtoDF returns a DiscoRhythm format data.frame.

Examples

df <- discoGetSimu()
se <- discoDFtoSE(df)

df <- discoSEtoDF(se) 

matthewcarlucci/DiscoRhythm documentation built on March 24, 2022, 10:22 a.m.