sequenceDesignMatrix          package:oligo          R Documentation

_C_r_e_a_t_e _d_e_s_i_g_n _m_a_t_r_i_x _f_o_r _s_e_q_u_e_n_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Creates design matrix for sequences.

_U_s_a_g_e:

     sequenceDesignMatrix(seqs)

_A_r_g_u_m_e_n_t_s:

    seqs: 'character' vector of 25-mers.

_D_e_t_a_i_l_s:

     This assumes all sequences are 25bp long.

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

_V_a_l_u_e:

     Matrix with length(seqs) rows and 75 columns.

_E_x_a_m_p_l_e_s:

     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)

