hlaGenoMFreq: Minor Allele Frequency

In HIBAG: HLA Genotype Imputation with Attribute Bagging

Description

To calculate the minor allele frequencies from genotypes or haplotypes.

Usage

hlaGenoMFreq(obj)

Arguments

obj	an object of hlaSNPGenoClass

Value

Return minor allele frequecies.

Author(s)

Xiuwen Zheng

See Also

hlaGenoAFreq, hlaGenoMFreq, hlaGenoMRate, hlaGenoMRate_Samp

Examples

summary(HapMap_CEU_Geno)

summary(hlaGenoMFreq(HapMap_CEU_Geno))

Example output

HIBAG (HLA Genotype Imputation with Attribute Bagging)
Kernel Version: v1.5 (64-bit, AVX2)
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/G C/T G/T A/C 
655 632 141 136 
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.0000  0.1071  0.2054  0.2276  0.3393  0.5000 

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