DOfamSKATRC: DofamSKATRC call back function

In Mega2R: Accessing and Processing a 'Mega2' Genetic Database

DofamSKATRC call back function

Description

Convert the genotypesraw() allele patterns of 0x10001, 0x10002 (or 0x20001), 0x20002, 0 to the numbers 0, 1, 2, 9 for each marker. (Reverse, the order iff allele "1" has the minor allele frequency.) Ignore markers that have no variants. Finally, invoke famSKAT_RC with the converted genotype matrix. Save information about the range and the p.value calculated by famSKAT_RC in envir$famSKATRC_results. If you want to change the argument values to this function they should be changed instead when calling the Mega2famSKATRC function.

Usage

DOfamSKATRC(
  markers_arg,
  range_arg,
  envir,
  pheno = 3,
  id = NULL,
  covariates = NULL,
  sqrtweights_c = NULL,
  sqrtweights_r = NULL,
  binomialimpute = TRUE,
  acc = 1e-06,
  maf = 0.05,
  phi = c(0, 0.2, 0.5, 0.9)
)

Arguments

markers_arg	a data.frame with the following 5 observations: locus_link is the ordinal ranking of this marker among all loci locus_link_fill is the position of corresponding genotype data in the unified_genotype_table MarkerName is the text name of the marker chromosome is the integer chromosome number position is the integer base pair position of marker
range_arg	one row of a ranges_arg. The latter is a data frame of at least three integer columns. The columns indicate a range: a chromosome number, a start base pair value, and an end base pair value.
envir	'environment' containing SQLite database and other globals especially the phenotype_table, phe.
pheno	is an index into the phenotypes_table to select the phenotype. Missing phenotypes are represented by NA.
id	a vector of individuals to be included in the test, a subset of the family members. If NULL is given, all members will be used.
covariates	a matrix of covariates for the phenotype.
sqrtweights_c	weight function for common variants, if NULL use weight set in init_famSKAT
sqrtweights_r	weight function for rare variants, if NULL use weight set in init_famSKAT.
binomialimpute	if TRUE, impute missing genotypes using a binomial distribution.
acc	accuracy used in Davies approximation.
maf	threshold used to separate rare from common variants.
phi	a vector of ratios ratios; each indicates the contribution of rare variants.

Value

None

Note

This function accumulates output in the data frame, envir$famSKATRC_results. It will print out the lines as they are generated if envir$verbose is TRUE. It does not write the data frame to a file. You must save the data frame. You also must initialize the data frame when necessary.

See Also

init_famSKATRC, Mega2famSKATRC

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_famSKATRC(db, verbose = TRUE)
ENV$famSKATRC_results = ENV$famSKATRC_results[0, ]
Mega2famSKATRC(gs=1:1, envir=ENV, pheno=3)
# this sets one of the many arguments for DOfamSKATRC
# but basically prepares the ENV for the direct use of DOfamSKATRC (below).


# donttestcheck: try this below instead if there is time
 Mega2famSKATRC(genes=c("CEP104"), envir=ENV, pheno=3 )


# DOfamSKATRC is called within Mega2famSKATRC. init_famSKATRC and Mega2famSKATRC need to be
# called to set up the environment for famSKAT_RC to run.  BUT, you should ignore DOfamSKATRC
# and use Mega2famSKATRC instead.
#
applyFnToRanges(DOfamSKATRC, ENV$refRanges[50:60, ], ENV$refIndices, envir=ENV)
# this will use all the default argument values for DOfamSKATRC

Mega2R documentation built on May 29, 2024, 1:14 a.m.