desMarkers           package:GeneticsBase           R Documentation

_D_e_s_c_r_i_p_t_i_v_e _s_t_a_t_i_s_t_i_c_s _f_o_r _m_a_r_k_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     Descriptive statistics for markers.

_U_s_a_g_e:

     desMarkers(geneSetObj,
                founderOnly=TRUE,
                thrsh=0.05,
                HWE.method=c("simulate","exact"),
                simulate.p.value=FALSE,
                B=10000,
                markerThrsh=100,
                maxDist=5,
                LDmeasure="r2",
                plot=TRUE,
                ...)

_A_r_g_u_m_e_n_t_s:

geneSetObj: a 'geneSet' object.

founderOnly: indicates if using only founder info

   thrsh: threshold for Hardy-Weinberg equilibrium test. If the pvalue
          of the HWE test for a marker is greater than 'thrsh', then
          the marker is a good marker.

HWE.method: method to do Hardy-Weinberg equilibrium test.

simulate.p.value: indicates if the pvalue of the HWE test is calculated
          by Monte Carlo simulation. 'simulate.p.value=FALSE' means the
          pvalue is calculated from asymptotic chi-squared distribution
          of the test statistic. Otherwise, Monte Carlo simulation is
          used to calculate pvalue. For more details, please refers to
          the 'R' function 'chisq.test'.

       B: the number of replicates used in Monte Carlo simulation to
          get the pvalue of HWE test. For more details, please refers
          to the 'R' function 'chisq.test'.

markerThrsh: if the number of markers is greater than this threshold,
          then 'LDdist' is called instead of 'LD'.

 maxDist: the width of window used in 'LDdist' function.

LDmeasure: indicates if 'r^2' or 'D'' is to be plot.

    plot: indicates if LD plot is output or not.

     ...: Other arguments that are used by HWE.chisq or HWE.exact.

_V_a_l_u_e:

     a data frame contains components:  

    Name: marker names

Position: marker positions

  ObsHET: marker's observed heterozygosity (i.e., proportion of
          heterozygotes at markes). Missing alleles are excluded in the
          calculation.

 PredHET: marker's predicted heterozygosity (i.e., '2*MAF*(1-MAF)').
          Missing alleles are excluded in the calculation.

  HWpval: pvalues for Hardy-Weinberg test

   pGeno: percentage of non-missing genotypes for markes

     MAF: minor allele frequencies. missing allele are excluded from
          calculation

  Rating: 'Rating[i]=1' means that the $i$-th marker passes HW test (do
          not reject H0 that HW equilibrium holds). 'Rating[i]=0' means
          HW equilibrum does hold for the $i$-th marker.

_A_u_t_h_o_r(_s):

     Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus
     ross.lazarus@channing.harvard.edu

_E_x_a_m_p_l_e_s:

       #data(CAMP)
       #res<-desMarkers(CAMP)
       #print(res)

