GeneInfo: Get the gene annotation table or add additional columns to it

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Get the gene annotation table or add additional columns to it

Description

The gene annotation table contains meta information for the rows of a grandR object. When loaded from the GRAND-SLAM output, this this contains gene ids, gene symbols, the transcript length and the type.

Usage

GeneInfo(data, column = NULL, value = NULL)

GeneInfo(data, column) <- value

Arguments

data	A grandR object
column	The name of the additional annotation column
value	The additional annotation per gene

Details

New columns can be added either by data<-GeneInfo(data,name,values) or by GeneInfo(data,name)<-values.

Value

Either the gene annotation table or a new grandR object having an updated gene annotation table

See Also

Genes, Coldata, ReadGRAND

Examples

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

head(GeneInfo(sars))
GeneInfo(sars,"LengthCategory")<-cut(GeneInfo(sars)$Length,c(0,1500,2500,Inf),
                                          labels=c("Short","Medium","Long"))
table(GeneInfo(sars)$LengthCategory)

grandR documentation built on April 4, 2025, 2:27 a.m.