Analysis table functions

Get analysis names and add or remove analyses

Usage

Analyses(data, description = FALSE)

AddAnalysis(data, name, table, by = NULL, 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
by: Specify a column that contains gene names or symbols (see details)
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

Value

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

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 in most cases 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).

If it is called by the user (e.g. to add analysis results from external tools or from the literature, see pulse-chase vignette), then the user must make sure that either the rownames of the given table can be recognized as genes (names or symbols), or that there is a column in the table giving genes (this must be specified as the "by" parameter). The table does neither have to be sorted the same way the grandR object is, nor does it have to be complete. AddAnalysis will take care or reordering and inserting NA for missing genes (and it will issue a warning in case of missing genes).

Functions

Analyses(): Obtain the analyses names
AddAnalysis(): Add an analysis table
DropAnalysis(): Remove analyses from the grandR object

Examples

sars <- ReadGRAND(system.file("extdata", "sars.tsv.gz", package = "grandR"),
                  design=c("Cell",Design$dur.4sU,Design$Replicate))
#> Warning: Duplicate gene symbols (n=1, e.g. MATR3) present, making unique!

sars <- Normalize(sars)     # default behavior is to update the default slot; this calls AddSlot
Slots(sars)
#> [1] "count" "ntr"   "alpha" "beta"  "norm" 
DefaultSlot(sars)
#> [1] "norm"
sars <- DropSlot(sars,"norm")
sars                        # note that the default slot reverted to count
#> grandR:
#> Read from /tmp/RtmpzQAFxV/temp_libpath746d2bf75aeb/grandR/extdata/sars
#> 1045 genes, 12 samples/cells
#> Available data slots: count,ntr,alpha,beta
#> Available analyses: 
#> Available plots: 
#> Default data slot: count