computeDosage {Mega2R}

computeDosage 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.)

Usage

computeDosage(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 especially the phenotype_table, phe.

Value

a matrix of samples X markers for all the markers that have nonzero changes.

See Also

DOfamSKATRC

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_famSKATRC(db, verbose = TRUE)
dimDosage = function(m, r, e) {print(dim(computeDosage(m, r, e)))}
applyFnToRanges(dimDosage, ENV$refRanges[50:60, ], ENV$refIndices, envir=ENV)
# This will use return dosage matrices for the markers in the ranges 50 - 60,
# but is basically ignores the results.