hlaGenoAFreq: Allele Frequency

In HIBAG: HLA Genotype Imputation with Attribute Bagging

Description

To calculate the allele frequencies from genotypes or haplotypes.

Usage

hlaGenoAFreq(obj)

Arguments

obj	an object of hlaSNPGenoClass

Value

Return allele frequecies.

Author(s)

Xiuwen Zheng

See Also

hlaGenoAFreq, hlaGenoMFreq, hlaGenoMRate, hlaGenoMRate_Samp

Examples

summary(HapMap_CEU_Geno)

summary(hlaGenoAFreq(HapMap_CEU_Geno))

Example output

HIBAG (HLA Genotype Imputation with Attribute Bagging)
Kernel Version: v1.3
Supported by Streaming SIMD Extensions (SSE2) [64-bit]
SNP genotypes: 
	60 samples X 1564 SNPs
	SNPs range from 25769023bp to 33421576bp on hg19
Missing rate per SNP:
	min: 0, max: 0.0666667, mean: 0.0651215, median: 0.0666667, sd: 0.00968287
Missing rate per sample:
	min: 0, max: 0.969949, mean: 0.0651215, median: 0.000639386, sd: 0.243737
Minor allele frequency:
	min: 0, max: 0.5, mean: 0.227582, median: 0.205357, sd: 0.1389
Allelic information:
A/C A/G C/T G/T 
136 655 632 141 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.1964  0.4911  0.4894  0.7768  1.0000 

HIBAG documentation built on March 24, 2021, 6 p.m.