getNgsColorsInfo            package:oligo            R Documentation

_H_e_l_p_e_r _f_u_n_c_t_i_o_n _t_o _e_x_t_r_a_c_t _c_o_l_o_r _i_n_f_o_r_m_a_t_i_o_n _f_o_r _f_i_l_e_n_a_m_e_s _o_n
_N_i_m_b_l_e_G_e_n _a_r_r_a_y_s.

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

     This function will (try to) extract the color information for
     NimbleGen arrays. This is useful when using 'read.xysfiles2' to
     parse XYS files for Tiling applications.

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

     getNgsColorsInfo(path = ".", pattern1 = "_532", pattern2 = "_635", ...)

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

    path: path where to look for files

pattern1: pattern to match files supposed to go to the first channel

pattern2: pattern to match files supposed to go to the second channel

     ...: extra arguments for 'list.xysfiles'

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

     Many NimbleGen samples are identified following the pattern
     sampleID_532.XYS / sampleID_635.XYS.

     The function suggests sample names if all the filenames follow the
     standard above.

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

     A data.frame with, at least, two columns: 'channel1' and
     'channel2'. A third column, 'sampleNames', is returned if the
     filenames follow the sampleID_532.XYS / sampleID_635.XYS standard.

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

     Benilton Carvalho <bcarvalh@jhsph.edu>

