Analyses {grandR}R Documentation

Analysis table functions

Description

Get analysis names and add or remove analyses

Usage

Analyses(data, description = FALSE)

AddAnalysis(data, name, table, warn.present = TRUE)

DropAnalysis(data, pattern = NULL)

Arguments

data

A grandR object

description

if TRUE, also return the column names of each analysis table (i.e. a list named according to the analyses)

name

The user-defined analysis name

table

The analysis table to add

warn.present

Warn if an analysis with the same name is already present (and then overwrite)

pattern

A regular expression that is matched to analysis names

Details

The columns in the analysis tables are defined by the analysis method (e.g. "Synthesis","Half-life" and "rmse" by FitKinetics). A call to an analysis function might produce more than one table (e.g. because kinetic modeling is done for multiple Conditions). In this case, AddAnalysisTable produces more than one analysis table.

AddAnalysis is usually not called directly by the user, but is used by analysis methods to add their final result to a grandR object (e.g., FitKinetics,LikelihoodRatioTest,LFC,PairwiseDESeq2).

Value

Either the analysis names or a grandR data with added/removed slots or the metatable to be used with AddAnalysis

Functions

See Also

Slots, DefaultSlot

Examples

sars <- ReadGRAND(system.file("extdata", "sars.tsv.gz", package = "grandR"),
                  design=c("Cell",Design$dur.4sU,Design$Replicate))

sars <- Normalize(sars)     # default behavior is to update the default slot; this calls AddSlot
Slots(sars)
DefaultSlot(sars)
sars <- DropSlot(sars,"norm")
sars                        # note that the default slot reverted to count


[Package grandR version 0.2.0 Index]