error.correction          package:sagenhaft          R Documentation

_E_s_t_i_m_a_t_e _s_e_q_u_e_n_c_i_n_g _e_r_r_o_r_s _a_n_d _c_o_m_p_u_t_e _c_o_r_r_e_c_t_e_d _c_o_u_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     These functions are used to compute sequencing error correction in
     a library. They are automatically called when extracting tags from
     sequences and therefore usually do not have to be called directly.

_U_s_a_g_e:

     estimate.errors.mean(lib)
     compute.sequence.neighbors(tags, taglength=10, quality.scores=NULL,
                                output="character") 
     em.estimate.error.given(lib, maxstep=50, ...)

_A_r_g_u_m_e_n_t_s:

     lib: A sage library object

    tags: A character vector or numeric vector containing tags

taglength: length of tag

quality.scores: A matrix containing base quality scores as -10 log10 Pe

 maxstep: iterations of EM algorithm

  output: Output type for 'compute.sequence.neighbors', either
          character or numeric

     ...: Other arguments ignored.

_A_u_t_h_o_r(_s):

     Tim Beissbarth

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://tagcalling.mbgproject.org>

_S_e_e _A_l_s_o:

     'extract.lib', 'sage.library'

_E_x_a_m_p_l_e_s:

     library(sagenhaft)
     B6Hypo <-read.sage.library(system.file("data/B6HypothalHFI.sage",
                                package="sagenhaft")) 
     E15post <- read.sage.library(system.file("data/E15postHFI.sage",
                                  package="sagenhaft")) 
     testlib <- combine.libs(B6Hypo, E15post)
     testlib <- estimate.errors.mean(testlib)
     testlib <- em.estimate.error.given(testlib)
     tagneighbors <- compute.sequence.neighbors(testlib$seqs[,"seq"], 10,
                               testlib$seqs[,paste("q", 1:10, sep="")]) 

