Analyses {grandR} | R Documentation |
Get analysis names and add or remove analyses
Analyses(data, description = FALSE)
AddAnalysis(data, name, table, warn.present = TRUE)
DropAnalysis(data, pattern = NULL)
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 |
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).
Either the analysis names or a grandR data with added/removed slots or the metatable to be used with AddAnalysis
Analyses()
: Obtain the analyses names
AddAnalysis()
: Add an analysis table
DropAnalysis()
: Remove analyses from the grandR object
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