readIdatFiles             package:crlmm             R Documentation

_R_e_a_d_s _I_d_a_t _F_i_l_e_s _f_r_o_m _I_n_f_i_n_i_u_m _I_I _I_l_l_u_m_i_n_a _B_e_a_d_C_h_i_p_s

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

     Reads intensity information for each bead type from .idat files of
     Infinium II genotyping BeadChips

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

     readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path=".",
                   arrayInfoColNames=list(barcode="SentrixBarcode_A",
                                          position="SentrixPosition_A"),
                   highDensity=FALSE, sep="_",
                   fileExt=list(green="Grn.idat", red="Red.idat"),
                   saveDate=FALSE)

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

sampleSheet: 'data.frame' containing Illumina sample sheet information
          (for required columns, refer to BeadStudio Genotyping guide -
          Appendix A).

arrayNames: character vector containing names of arrays to be read in. 
          If 'NULL', all arrays that can be found in the specified
          working directory will be read in.

     ids: vector containing ids of probes to be read in.  If 'NULL' all
          probes found on the first array are read in.

    path: character string specifying the location of files to be read
          by the function

arrayInfoColNames: (used when 'sampleSheet' is specified) list
          containing elements 'barcode' which indicates column names in
          the 'sampleSheet' which contains the arrayNumber/barcode
          number and 'position' which indicates the strip number.  In
          older style sample sheets, this information is combined
          (usually in a column named 'SentrixPosition') and this should
          be specified as 'list(barcode=NULL,
          position="SentrixPosition")'

highDensity: logical (used when 'sampleSheet' is specified). If 'TRUE',
          array extensions '_A', '_B' in sampleSheet are replaced with
          'R01C01', 'R01C02' etc.

     sep: character string specifying separator used in .idat file
          names.

 fileExt: list containing elements 'Green' and 'Red' which specify the
          .idat file extension for the Cy3 and Cy5 channels.

saveDate: logical.  Should the dates from each .idat be saved with
          sample information?

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

     The summarised Cy3 (G) and Cy5 (R) intensity, number of beads that
     were used in each channel and standard errors (all on the orginal
     scale) are read in from the .idat files.

     Where available, a 'sampleSheet' data.frame, in the same format as
     used by BeadStudio (columns 'Sample_ID', 'SentrixBarcode_A' and
     'SentrixPosition_A' are required) which keeps track of sample
     information can be specified.

     Thanks to Keith Baggerly who provided the code to read in the
     binary .idat files.

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

     NChannelSet with intensity data ('R', 'G'), number of beads
     ('Rnb', 'Gnb') and standard errors ('Rse', 'Gse') for each bead
     type.

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

     Matt Ritchie

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

     #RG = readIdatFiles()

