sequenceDesignMatrix {oligo} | R Documentation

## Create design matrix for sequences

### Description

Creates design matrix for sequences.

### Usage

    sequenceDesignMatrix(seqs)

### Arguments

`seqs` | `character` vector of 25-mers.

### Details

This assumes all sequences are 25bp long.

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

### Value

Matrix with length(seqs) rows and 75 columns.

### 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)

[Package oligo version 1.48.0 Index]