The columns of a grandR object are samples or cells.
The column annotation table contains meta information for the columns of a grandR object.
When loaded from the GRAND-SLAM output, this this constructed from the sample/cell names by
MakeColdata
Arguments
- data
A grandR object
- column
The name of the additional annotation column; can also be a data frame (then value is ignored and the data frame is added)
- value
The additional annotation per sample or cell
Value
Either the column annotation table or a new grandR object having an updated column annotation table
Details
A new column can be added either by data<-Coldata(data,name,values) or by Coldata(data,name)<-values.
Several new columns can be added by data<-Coldata(data,df) where df is either a data frame or matrix.
The column named Condition has a special meaning in this table: It is used by several functions to stratify the columns
during the analysis (e.g. to estimate separate kinetic parameters with FitKinetics or it is used as covariate for
LFC or LikelihoodRatioTest). For that reason there are special functions to set and get this column.
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!
head(GeneInfo(sars))
#> Gene Symbol Length Type
#> 1 ENSG00000152332 UHMK1 8478 Cellular
#> 2 ENSG00000162772 ATF3 2103 Cellular
#> 3 ENSG00000090621 PABPC4 3592 Cellular
#> 4 ENSG00000185483 ROR1 5832 Cellular
#> 5 ENSG00000058673 ZC3H11A 11825 Cellular
#> 6 ENSG00000257315 ZBED6 12481 Cellular
GeneInfo(sars,"LengthCategory")<-cut(GeneInfo(sars)$Length,c(0,1500,2500,Inf),
labels=c("Short","Medium","Long"))
table(GeneInfo(sars)$LengthCategory)
#>
#> Short Medium Long
#> 73 160 812