merge                 package:limma                 R Documentation

_M_e_r_g_e _R_G_L_i_s_t _o_r _M_A_L_i_s_t _D_a_t_a _O_b_j_e_c_t_s

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

     Merge two microarray data sets represented by RGLists in possibly
     irregular order.

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

     ## S3 method for class 'RGList':
     merge(x,y,...)

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

       x: 'RGList-class' or 'MAList-class' object

       y: 'RGList' object, corresponding to the same genes as for 'x',
          possibly in a different order, but with different arrays.

     ...: other arguments are accepted but not used at present

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

     'RGList' and 'MAList' objects are list objects containing numeric
     matrices all of the same dimensions. The RGLists are merged by
     merging each of the components by row names or, if there are no
     row names, by IDs in the 'genes' component. Unlike when using
     'cbind', row names are not required to be in the same order or to
     be unique. In the case of repeated row names, the order of the
     rows with repeated names in preserved. This means that the first
     occurrence of each name in 'x$R' is matched with the first
     occurrence of the same name in 'y$R', the second with the second,
     and so on. The final vector of row names is the same as in 'x'.

     Note: if the 'RGList' objects contain the same number of genes in
     the same order then the appropriate function to combine them is
     'cbind' rather than 'merge'.

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

     An merged object of the same class as 'x' and 'y' with the same
     components as 'x'. Component matrices have the same rows names as
     in 'x' but columns from 'y' as well as 'x'.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     R base provides a 'merge' method for merging data.frames.

     An overview of limma commands for reading, subsetting and merging
     data is given in 03.ReadingData.

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

     M <- A <- matrix(11:14,4,2)
     rownames(M) <- rownames(A) <- c("a","a","b","c")
     MA1 <- new("MAList",list(M=M,A=A))

     M <- A <- matrix(21:24,4,2)
     rownames(M) <- rownames(A) <- c("b","a","a","c")
     MA2 <- new("MAList",list(M=M,A=A))

     merge(MA1,MA2)
     merge(MA2,MA1)

