Error while building ExpressionSet using Bioconductor - r

Question

I am trying to make ExpressionSet files for the analysis of RNA-seq data. I simply have a matrix of counts called "exprs", a data.frame of features (genes) called "features" and a data.frame of sample attributes called "phenotypes".
Here is the code I run to import all data into R and create a single "Object" of Expressionset. But it returns an error.
## DE object creation
### importing 3 data files to R first
### Count MATRIX
dataDirectory <- system.file("extdata", package="Biobase")
exprs <- as.matrix(read.table("counts.txt", sep = "\t", header = TRUE, row.names = 1, as.is = TRUE))
class(exprs)
head.matrix(exprs)
str(exprs)
Output:
num [1:40220, 1:20] 12.39 6.37 11.18 10.72 10.65 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:40220] "ENSG00000000003" "ENSG00000000005" "ENSG00000000419" "ENSG00000000457" ...
..$ : chr [1:20] "sample_1379_PNC" "sample_1360_PA_A" "sample_1412_PNB" "sample_1405_PA_A" ...
### Features data which contains gene names and symbols for each ensembl id (gene) -> DATAFRAME
features <- read.csv("features.txt", sep = "\t")
rownames(features) <- features$ID
features$ID <- NULL
str(features)
Output:
'data.frame': 40223 obs. of 2 variables:
$ Symbol : chr "TSPAN6" "TNMD" "DPM1" "SCYL3" ...
$ Symbol2: chr "TSPAN6" "TNMD" "DPM1" "SCYL3" ...
### Phenotype data which contains attributes for each sample -> DATAFRAME
phenotypes <- read.csv("phenotypes.txt", sep = "\t")
rownames(phenotypes) <- phenotypes$X1
phenotypes$X1 <- NULL
str(phenotypes)
Output:
'data.frame': 20 obs. of 2 variables:
$ condition: chr "normal" "tumor" "normal" "tumor" ...
$ type : chr "mono" "mono" "poly" "mono" ...
# Load package
library(Biobase)
# Create ExpressionSet object
eset <- ExpressionSet(assayData = exprs,
phenoData = annotatedDataFrameFrom(phenotypes),
featureData = annotatedDataFrameFrom(features))
Output:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘annotatedDataFrameFrom’ for signature ‘"character"’