R/expressionset-helpers.r
ExpressionSet-helpers.Rd
These functions present quick way to create ExpressionSet objects.
as.ExpressionSet(x, ...) # S4 method for data.frame as.ExpressionSet(x, annotation_cols = !sapply(x, is.double)) read.ExpressionSet(file, header = TRUE, ...)
x | data.frame to convert to an ExpressionSet. |
---|---|
... | Additional parameters to read.table |
annotation_cols | The data.frame columns used as annotations. All others are used as expressions. (Logical, character or numerical index array) |
file | File path to read ASCII data from |
header | Specifies if the file has a header row. |
an ExpressionSet object
They work by using all continuous (double) columns as expression data, and all others as observation annotations.
read.table on which read.ExpressionSet
is based, and ExpressionSet.
library(Biobase)#>#>#> #>#>#> #> #> #>#>#> #>#>#> #> #> #> #> #> #>#>#> #> #> #>df <- data.frame(Time = seq_len(3), #integer column Actb = c(0.05, 0.3, 0.8), Gapdh = c(0.2, 0.03, 0.1)) set <- as.ExpressionSet(df) rownames(exprs(set)) == c('Actb', 'Gapdh')#> [1] TRUE TRUE#> [1] TRUE TRUE TRUE