breaks              package:VanillaICE              R Documentation

_I_d_e_n_t_i_f_y _b_r_e_a_k_p_o_i_n_t_s _f_r_o_m _t_h_e _h_i_d_d_e_n _M_a_r_k_o_v _m_o_d_e_l _p_r_e_d_i_c_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     Identify breakpoints: physical position of breaks, number of SNPs
     in region, and the called hidden state.

_U_s_a_g_e:

     breaks(x, states, position, chromosome, sampleNames, chromosomeAnnotation = NULL, verbose = FALSE)

_A_r_g_u_m_e_n_t_s:

       x: Locus X sample matrix of hidden states where the hidden
          states are represented as integers

  states: Labels for the hidden states

position: Physical position of loci

chromosome: integer indicating chromosome (23=X)

sampleNames: sample labels

chromosomeAnnotation: chromosome annotation. see details

 verbose: verbose output

_D_e_t_a_i_l_s:

     One may provide their own chromosome annotation with centromere
     start and stop sites.  The format must be the same as the
     chromosomeAnnotation dataset in the R package SNPchip.

_V_a_l_u_e:

     data.frame

  sample: sample label

     chr: chromosome (23 = X)

   start: starting physical position of segment

     end: last physical position of segment

  nbases: number of bases in segment

 nprobes: number of probes in segment

   state: label for the state of the segment

_A_u_t_h_o_r(_s):

     R. Scharpf

_E_x_a_m_p_l_e_s:

     x <- matrix(rep(c(1, 2, 3, 1, 2), each=50), ncol=1)
     breaks(x, states=c("0", "1", "2"), position=1:nrow(x), chromosome=1,
            sampleNames="A")

