ds.alleleFrequency: Allelic frequency

In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

Allelic frequency

Description

Calculates the frequency of the A allele on a server side GenotypeData object.

Usage

ds.alleleFrequency(
  genoData,
  type = "combined",
  method = "fast",
  snpBlock = 5000L,
  datasources = NULL
)

Arguments

genoData	character Name of the GenotypeData object on the server
type	character (default "combined") Type of analysis, if ("split"), the frequencies will be calculated for each study server. If ("combined") a pooled methodology will be performed.
method	character (default "fast") If "fast" an optimized fast method will be used; if "slow" the function GWASTools::alleleFrequency will be used, this is notably slower.
snpBlock	integer (default 5000L) number of SNPs to read at each iteration, tune this parameter to improve performance. This argument is only used when method = "fast"
datasources	a list of DSConnection-class objects obtained after login.

Details

(From alleleFrequency documentation): Counts male heterozygotes on the X and Y chromosomes as missing values, and any genotype for females on the Y chromosome as missing values. A "sex" variable must be present in the scan annotation slot of genoData. Samples with missing sex are included in the allele counts for "all" and "MAF" for autosomes, but not for sex chromosomes.

Value

A data frame with a row for each SNP. Columns "M" for males, "F" for females, and "all" for all scans give frequencies of the A allele. Sample size for males, females, and all is returned as "n.M", "n.F", and "n", respectively. "MAF" is the minor allele frequency over all scans.

isglobal-brge/dsOmicsClient documentation built on March 20, 2023, 3:52 p.m.