Genes {grandR}

Gene and sample (or cell) names

Description

Get the genes and sample (or cell) names for a grandR object, or add an additional gene annotation column

Usage

Genes(data, genes = NULL, use.symbols = TRUE, regex = FALSE)

Columns(data, columns = NULL, reorder = FALSE)

Arguments

data

A grandR object

genes

which genes to use

use.symbols

obtain the gene symbols instead of gene names

regex

treat genes as a regex, and return all that match

columns

which columns (i.e. samples or cells) to return (see details)

reorder

if TRUE, do not enforce the current order of columns

Details

The genes are either the (often unreadable) gene ids (e.g. Ensembl ids), or the symbols.

Genes(data,use.symbols=FALSE) it the same as rownames(data), and Columns(data) is the same as colnames(data)

If both column and value are specified for GeneInfo, a new column is added to the gene annotation table

Columns can be given as a logical, integer or character vector representing a selection of the columns (samples or cells). The expression is evaluated in an environment having the Coldata, i.e. you can use names of Coldata as variables to conveniently build a logical vector (e.g., columns=Condition=="x").

Value

Either the gene or column names of the grandR data object, or the columns of an analysis table in the grandR object

See Also

Coldata, GeneInfo, Analyses

Examples

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

all(Genes(sars,use.symbols = FALSE)==rownames(sars))
all(Columns(sars)==colnames(sars))