hapmapchr22           package:GeneticsBase           R Documentation

_C_h_r_o_m_o_s_o_m_e _2_2 _g_e_n_o_t_y_p_e_s _f_r_o_m _I_n_t_e_r_n_a_t_i_o_n_a_l _H_a_p_M_a_p _p_r_o_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     The sample data file, hapmapchr22, contains genotypes of hromosome
     22 from the International HapMap project. This file contains
     genotypes from 30 CEPH trios (90 subjects) for all Phase 1 HapMap
     (about 1 SNP per 3kb on average) - see <URL: http://hapmap.org>
     for the original data file, full details of samples, markers and
     methods. Note that the HapMap data files are deidentified and
     freely distributable without restriction.

_U_s_a_g_e:

     data(hapmapchr22)

_F_o_r_m_a_t:

     The format is: chr "hapmapchr22"

_D_e_t_a_i_l_s:

     The file was created by converting chromosome 22 bulk data
     download data  files from the HapMap file repository at  <URL:
     http://hapmap.org/genotypes/2005-06_16c_phaseI/full/non-redundant/>

     Downloaded HapMap files were converted by transposing the layout
     of the data from one row per marker to the pedigree file
     convention of two columns per marker. There are many variants of
     the pedigree format but these files are compatible with the
     popular family based analysis software packages FBAT (<URL:
     http://www.biostat.harvard.edu/~fbat/fbat.htm>) and PBAT (<URL:
     http://www.biostat.harvard.edu/~clange/default.htm>)

     The file has a header row containing only the marker names
     followed by one row per subject.  Data rows always start with 6
     fields - 'family_id', 'individual_id', 'father_id', 'mother_id',
     gender and affection status. Parents have zero for 'mother_id' and
     'father_id'. The remaining columns in each row contain two allele
     codes for each marker. Alleles are coded as $0$ for missing,
     $1=A$, $2=C$, $3=G$ and $4=T$.  All fields in a row are delimited
     by one or more spaces. Note that affection status was arbitrarily
     set to 2 (affected) for children and 1 (unaffected) for adults -
     although in reality, HapMap CEPH subjects were not ascertained for
     any disease.

_S_o_u_r_c_e:

     <URL:
     http://hapmap.org/genotypes/2005-06_16c_phaseI/full/non-redundant/>

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.biostat.harvard.edu/~fbat/fbat.htm> <URL:
     http://www.biostat.harvard.edu/~clange/default.htm>

_E_x_a_m_p_l_e_s:

     data(hapmapchr22)

