DOSKAT: SKAT call back function

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

SKAT 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 (unless allMarkers is TRUE). Finally, invoke SKAT with the converted genotype matrix, Null model saved in envir$obj, and any additionally supplied arguments. Save information about the range and the p.value calculated by SKAT in envir$SKAT_results.

Usage

DOSKAT(markers_arg, range_arg, envir, ...)

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
...	extra arguments for SKAT

Value

None

Note

This function accumulates output in the data frame, envir$SKAT_results. It will print out the lines as they are generated if envir$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_SKAT, Mega2SKAT

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_SKAT(db, verbose = TRUE, allMarkers = FALSE)
Mega2SKAT(ENV$phe[, 3] - 1 ~ 1, "D", gs=1:1)


# donttestcheck: try this below instead if there is time
Mega2SKAT(ENV$phe[, 3] - 1 ~ 1, "D", kernel = "linear.weighted", 
          weights.beta = c(0.5, 0.5), genes=c("CEP104") )


# DOSKAT is called internally to Mega2SKAT. init_SKAT and Mega2SKAT need to be
# called to set up the environment for DOSKAT to run.  You should ignore DOSKAT
# and use Mega2SKAT instead
#
applyFnToRanges(DOSKAT, ENV$refRanges[50:60, ], ENV$refIndices)

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