set.stats: Basic statistics for a 'bed.matrix'

In gaston: Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Basic statistics for a bed.matrix

Description

Return an updated bed.matrix with new variables for several basic statistics.

Usage

set.stats(x, set.p = TRUE, set.mu_sigma = TRUE, 
          verbose = getOption("gaston.verbose",TRUE))

set.stats.snps(x, set.p = TRUE, set.mu_sigma = TRUE, 
               verbose = getOption("gaston.verbose",TRUE)) 

set.stats.ped(x, verbose = getOption("gaston.verbose",TRUE))

Arguments

x	A bed.matrix
set.p	If TRUE, x@p is updated
set.mu_sigma	If TRUE, x@mu and x@sigma are updated
verbose	If TRUE, display information on the function actions

Details

set.stats is called by default by all functions that create a bed.matrix, unless the global option gaston.auto.set.stats is FALSE (cf example below).

set.stats and set.stats.ped update x@ped, adding the following variables:

• N0, N1, N2 and NAs give for each individual the number of autosomal SNPs with a genotype equal to 0, 1, 2 and missing, respectively

• N0.x, N1.x, N2.x and NAs.x idem for chromosome X

• N0.y, N1.y, N2.y and NAs.y idem for chromosome Y

• N0.mt, N1.mt, N2.mt and NAs.mt idem for mitochondrial SNPs

• callrate, callrate.x, callrate.y, callrate.mt is the individual callrate for autosomal, X, Y, mitochondrial SNPs

• hz, hz.x, hz.y, hz.mt is the individual heterozygosity for autosomal, X, Y, mitochondrial SNPs

set.stats and set.stats.snps update x@snps, adding the following variables:

• N0, N1, N2 and NAs give for each SNP the number of individuals with a genotype equal to 0, 1, 2 and missing, respectively

• N0.f, N1.f, N2.f and NAs.f give, only for SNPs on chromosome X, the number of female individuals with a genotype equal to 0, 1, 2 and missing, respectively

• callrate is the SNP callrate (for Y linked SNPs, the callrate is computed usin males only).

• maf is the Minor Allele Frequency

• hz is the SNP heterozygosity (for X linked SNPs, the heterozygosity is computed using females only).

If set.p = TRUE, x@p is updated with the alternate allele frequency.

If set.mu_sigma = TRUE, x@mu is updated with the genotype mean (equal to 2*x@p) and x@sigma with the genotype standard deviation (should be approximately sqrt(2*x@p*(1-x@p)) under Hardy-Weinberg Equilibrium).

Value

A bed.matrix similar to x, with slots updated as described above.

Author(s)

Hervé Perdry and Claire Dandine-Roulland

See Also

set.hwe, set.genomic.sex

Examples

# Disable auto set stats :
options(gaston.auto.set.stats = FALSE)

# Load data
data(TTN)
x <- as.bed.matrix(TTN.gen, TTN.fam, TTN.bim)
str(x@ped)
str(x@snps)

# Compute statistics
x <- set.stats(x)
str(x@ped)
str(x@snps)

# restore default behavior
options(gaston.auto.set.stats = TRUE)

gaston documentation built on May 29, 2024, 7:33 a.m.