blurGenotype {GenABEL} | R Documentation |

## blur genotype calls into probabilites...

### Description

blur genotype calls into probabilites

### Usage

blurGenotype(g, q, epsilon=0.01)

### Arguments

`g` |
vector of genotypes for a particular person
(at locus 1, locus 2, etc., coded as 0, 1, 2 (corresponding
to genotypes AA, AB, and BB, respectively) and NA. |

`q` |
(optional) vector of coded allele freqeuncies for
locus 1, locus 2, etc. |

`epsilon` |
error rate |

### Details

'blurs' genotype calls into probabilities: translates
single genotype g2, into probability distribution P(g1|g2),
that is probability that true genotype is g1
given g2 is the observed 'called' genotype and error rate is
epsilon. Probability that 'true' genotype is called genotype
is set to (1-epsilon)^2, the probability that true genotype
differs at 1 allele is set to epsilon*(1-epsilon), and
both allelel differ = epsilon^2.

### Value

matrix with columns corresponding to SNPs
and rows corresponding to 'g0', 'g1', 'g2'. For
a particular SNP, a vale in cell 'gK' is the
probability that true genotype is 'K', given
thw original call and error-rate.

### Author(s)

Yurii Aulchenko

### Examples

data(srdta)
# select 10 first SNPs
df <- srdta[,1:10]
# compute effect allele freq
EAF <- summary(gtdata(df))$"Q.2"
EAF
# get genotypes of first 5 people
g1 <- as.numeric(df[1:5,])
g1
# blur the genotype of person 1, snp 1
blurGenotype(g1[1,1])
# blur all genotypes of person 2; assume no info for missing
blurGenotype(g1[2,])
# blur all genotypes of person 2; use HWE to infer missing
blurGenotype(g1[2,],q=EAF)

[Package

*GenABEL* version 1.6-7

Index]