descriptives.marker: Function to generate descriptive summary tables for genotypic...

In GenABEL: genome-wide SNP association analysis

Description

Function to generate descriptive summary tables for genotypic data

Usage

	descriptives.marker(data,snpsubset,idsubset,file,mafc,hwec,snpc,idcc,digits = 3)

Arguments

data	an object of snp.data-class or gwaa.data-class
snpsubset	Index, character or logical vector with subset of SNPs to run analysis on. If missing, all SNPs from data are used for analysis.
idsubset	Index, character or logical vector with subset of IDs to run analysis on. If missing, all people from data are used for analysis.
file	A string specifying the name of a file to write the tables to (default is missing).
mafc	vector containing desired cut-off levels for minor allele frequency
hwec	vector containing desired cut-off levels for exact HWE P-values
snpc	vector containing desired cut-off levels for SNP call rate
idcc	vector containing desired cut-off levels for individual SNP call rate
digits	number of digits to be printed

Value

A list containing descriptive tables and statistics

Author(s)

Yurii Aulchenko

Examples

	require(GenABEL.data)
	data(srdta)
	descriptives.marker(srdta)

Example output

Loading required package: MASS
Loading required package: GenABEL.data
$`Minor allele frequency distribution`
     X<=0.01 0.01<X<=0.05 0.05<X<=0.1 0.1<X<=0.2 X>0.2
No    22.000       54.000     107.000     150.00 500.0
Prop   0.026        0.065       0.128       0.18   0.6

$`Cumulative distr. of number of SNPs out of HWE, at different alpha`
     X<=1e-04 X<=0.001 X<=0.01 X<=0.05 all X
No      2.000    2.000   9.000  32.000   833
Prop    0.002    0.002   0.011   0.038     1

$`Distribution of proportion of successful genotypes (per person)`
     X<=0.9 0.9<X<=0.95 0.95<X<=0.98 0.98<X<=0.99 X>0.99
No        0     1199.00      1301.00            0      0
Prop      0        0.48         0.52            0      0

$`Distribution of proportion of successful genotypes (per SNP)`
     X<=0.9 0.9<X<=0.95 0.95<X<=0.98 0.98<X<=0.99 X>0.99
No        0     415.000      418.000            0      0
Prop      0       0.498        0.502            0      0

$`Mean heterozygosity for a SNP`
[1] 0.3302776

$`Standard deviation of the mean heterozygosity for a SNP`
[1] 0.1498426

$`Mean heterozygosity for a person`
[1] 0.3309457

$`Standard deviation of mean heterozygosity for a person`
[1] 0.04206737

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