summary.snp.data: function to summary GWAA data

In GenABEL: genome-wide SNP association analysis

Description

Provides summary of an object of class snp.data-class. Chromosome, map position, allele coding, number of observed genotypes, allelic frequency, genotypic distrbution, P-value of the exact test for HWE, Fmax (estimate of deviation from HWE, allowing meta-analysis) and LRT P-value for HWE test are listed

Usage

	## S3 method for class 'snp.data'
summary(object, ...)

Arguments

object	snp.data object
...	additional arguments (not used)

Value

Data frame summary for snp.data object

Note

The P-values reported for X-chromosome are based on analysis of female data, but other statistics (frequencies, calls, ...) are based on all data. Statistics for Y-chromosome are based on male-only. P-HWE is not defined for mt- and Y- markers (set to 1.0).

Author(s)

Yurii Aulchenko

References

Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 76: 887-93.

See Also

summary.gwaa.data, snp.data-class

Examples

require(GenABEL.data)
data(srdta)
summary(gtdata(srdta[,1:20]))

Example output

Loading required package: MASS
Loading required package: GenABEL.data
      Chromosome Position Strand A1 A2 NoMeasured CallRate        Q.2 P.11 P.12
rs10           1     2500      +  T  G       2384   0.9536 0.13255034 1792  552
rs18           1     3500      +  G  A       2385   0.9540 0.28029350 1232  969
rs29           1     5750      -  G  T       2374   0.9496 0.13774221 1763  568
rs65           1    13500      +  A  T       2378   0.9512 0.71972246  182  969
rs73           1    14250      +  A  G       2385   0.9540 0.01341719 2331   44
rs114          1    24500      +  A  T       2393   0.9572 0.11679900 1868  491
rs128          1    27000      -  G  T       2391   0.9564 0.02488499 2281  101
rs130          1    27250      +  A  G       2379   0.9516 0.69377890  222 1013
rs143          1    31000      +  T  G       2377   0.9508 0.47728229  655 1175
rs150          1    33250      +  C  A       2369   0.9476 0.65998312  267 1077
rs179          1    41500      -  G  T       2365   0.9460 0.44059197  732 1182
rs183          1    42500      +  A  T       2363   0.9452 0.20969107 1479  777
rs186          1    43000      +  A  G       2376   0.9504 0.07954545 2011  352
rs200          1    47000      +  A  T       2384   0.9536 0.25482383 1317  919
rs239          1    57750      -  A  G       2369   0.9476 0.24715070 1344  879
rs245          1    60500      +  A  T       2380   0.9520 0.15021008 1725  595
rs298          1    76250      +  C  A       2362   0.9448 0.03513971 2200  158
rs300          1    77000      +  A  C       2383   0.9532 0.12861939 1807  539
rs312          1    78500      -  G  A       2370   0.9480 0.33291139 1039 1084
rs324          1    82500      +  G  C       2365   0.9460 0.55813953  454 1182
      P.22       Pexact         Fmax         Plrt
rs10    40 7.897327e-01 -0.006880004 7.355343e-01
rs18   184 7.608230e-01 -0.007017332 7.315304e-01
rs29    43 7.955141e-01 -0.007241148 7.227853e-01
rs65  1227 6.475412e-01 -0.010016746 6.246577e-01
rs73    10 1.792470e-12  0.303150234 1.281239e-12
rs114   34 7.663683e-01  0.005487764 7.894076e-01
rs128    9 9.408599e-06  0.129600629 1.000431e-05
rs130 1144 9.615127e-01 -0.002140946 9.168114e-01
rs143  547 6.512540e-01  0.009313705 6.497695e-01
rs150 1025 5.518478e-01 -0.012948436 5.281254e-01
rs179  451 5.314637e-01 -0.013890521 4.992849e-01
rs183  107 7.095590e-01  0.007911363 7.013030e-01
rs186   13 6.744629e-01 -0.011692468 5.610005e-01
rs200  148 4.835439e-01 -0.015033259 4.614783e-01
rs239  146 8.686118e-01  0.002933954 8.865215e-01
rs245   60 2.974640e-01  0.020736989 3.178111e-01
rs298    4 5.332414e-01  0.013528445 5.321997e-01
rs300   37 7.151055e-01 -0.009067916 6.555613e-01
rs312  247 1.519431e-01 -0.029766500 1.462321e-01
rs324  729 5.319219e-01 -0.013277512 5.184146e-01

GenABEL documentation built on May 30, 2017, 3:36 a.m.