oligo (version 1.36.1)

sequenceDesignMatrix: Create design matrix for sequences

Description

Creates design matrix for sequences.

Usage

sequenceDesignMatrix(seqs)

Arguments

seqs

character vector of 25-mers.

Value

• Matrix with length(seqs) rows and 75 columns.

Details

This assumes all sequences are 25bp long.

The design matrix is often used when the objecive is to adjust intensities by sequence.

Examples

genSequence <- function(x)
    paste(sample(c("A", "T", "C", "G"), 25, rep=TRUE), collapse="", sep="")
seqs <- sapply(1:10, genSequence)
X <- sequenceDesignMatrix(seqs)
Y <- rnorm(10, mean=12, sd=2)
Ydemean <- Y-mean(Y)
X[1:10, 1:3]
fit <- lm(Ydemean~X)
coef(fit)