descriptives.scan: Function to describe "top" hits in GWA scan

In GenABEL: genome-wide SNP association analysis

Description

Describes "top" hits in GWA scan

Usage

	descriptives.scan(data,file,top=10,sortby="P1df", sep ="\t")

Arguments

data	an object of snp.data-class or gwaa.data-class
file	A string specifying the name of a file to write the tables to (default is no file output).
top	How many "top" hits to describe
sortby	How to pick up "top" hits ("P1df","P2df","Pgw1df","Pgw2df")
sep	field separator (takes effect only if file argument provided)

Value

A descritive table

Author(s)

Yurii Aulchenko

Examples

	require(GenABEL.data)
	data(srdta)
	x <- qtscore(qt2,srdta)
	descriptives.scan(x)

Example output

Loading required package: MASS
Loading required package: GenABEL.data
Summary for top 10 results, sorted by P1df 
       Chromosome Position Strand A1 A2    N      effB   se_effB  chi2.1df
rs6304          1  1682000      -  C  A 2383 25.253830 5.4125779 21.769387
rs8063          1  2169000      -  A  T 2378 10.677169 2.5728297 17.222261
rs2181          1   552000      -  C  G 2371 14.515723 4.1761739 12.081482
rs2082          1   525500      +  G  A 2366 -3.961485 1.2218493 10.511889
rs5620          1  1479750      -  C  T 2371  4.690274 1.4831586 10.000490
rs4887          1  1294750      +  C  G 2382  4.582004 1.4737387  9.666516
rs2597          1   666250      -  T  G 2374  6.326115 2.0363167  9.651250
rs2578          1   661750      +  C  G 2370 -2.509899 0.8219301  9.324868
rs3127          1   813250      +  G  C 2366  6.182779 2.0265095  9.308296
rs6585          1  1759000      -  A  T 2369  3.027642 1.0161412  8.877710
               P1df       effAB        effBB  chi2.2df          P2df
rs6304 3.074671e-06  25.2538304           NA  21.76939  3.074671e-06
rs8063 3.325171e-05  -0.8222893 882.13842034 790.78132 1.923168e-172
rs2181 5.092510e-04  14.5157235           NA  12.08148  5.092510e-04
rs2082 1.186090e-03 -11.0704842 -13.65050138  13.84179  9.869451e-04
rs5620 1.564985e-03   5.8581965  -0.01630937  12.83114  1.635890e-03
rs4887 1.876569e-03   6.2615562  -0.29005872  13.80709  1.004219e-03
rs2597 1.892227e-03   7.1524294  -0.50286720  11.03941  4.007034e-03
rs2578 2.260646e-03  -8.8181105  -8.73094382  21.67939  1.960562e-05
rs3127 2.281185e-03   7.2313179  -0.34328525  11.02811  4.029733e-03
rs6585 2.886735e-03   0.8828222   9.38926817  14.65736  6.564389e-04
              Pc1df
rs6304 2.743524e-05
rs8063 1.913618e-04
rs2181 1.782756e-03
rs2082 3.565794e-03
rs5620 4.476857e-03
rs4887 5.196690e-03
rs2597 5.232280e-03
rs2578 6.055655e-03
rs3127 6.100829e-03
rs6585 7.403359e-03

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