makeContrasts             package:limma             R Documentation

_C_o_n_s_t_r_u_c_t _M_a_t_r_i_x _o_f _C_u_s_t_o_m _C_o_n_t_r_a_s_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Construct the contrast matrix corresponding to specified contrasts
     of a set of parameters.

_U_s_a_g_e:

     makeContrasts(..., contrasts=NULL, levels) 

_A_r_g_u_m_e_n_t_s:

     ...: expressions, or character strings which can be parsed to
          expressions, specifying contrasts

contrasts: character vector specifying contrasts

  levels: character vector or factor giving the names of the parameters
          of which contrasts are desired, or a design matrix or other
          object with the parameter names as column names.

_D_e_t_a_i_l_s:

     This function expresses contrasts between a set of parameters as a
     numeric matrix. The parameters are usually the coefficients from a
     linear model fit, so the matrix specifies which comparisons
     between the coefficients are to be extracted from the fit. The
     output from this function is usually used as input to
     'contrasts.fit'. The contrasts can be specified either as
     expressions using '...' or as a character vector through
     'contrasts'. (Trying to specify contrasts both ways will cause an
     error.)

     The parameter names must be syntactically valid variable names in
     R and so, for example, must begin with a letter rather than a
     numeral. See 'make.names' for a complete specification of what is
     a valid name.

_V_a_l_u_e:

     Matrix which columns corresponding to contrasts.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     An overview of linear model functions in limma is given by the
     help page 06.LinearModels.

_E_x_a_m_p_l_e_s:

     makeContrasts(B-A,C-B,C-A,levels=c("A","B","C"))
     makeContrasts(contrasts="A-(B+C)/2",levels=c("A","B","C"))
     x <- c("B-A","C-B","C-A")
     makeContrasts(contrasts=x,levels=c("A","B","C"))