DOpedgene {Mega2R} | R Documentation |
pedgene call back function
Description
First, ignore call backs that have less than two markers. Second, convert the genotypesraw()
patterns of 0x10001, 0x10002 (or 0x20001), 0x20002, 0 from the genotype matrix
to the numbers 0, 1, 2, 0 for each marker. (Reverse, the order iff allele "1" has the
minor allele frequency.) Next, prepend the pedigree and person columns of the family data
to this modified genotype matrix. Finally, invoke pedgene
with the family data and
genotype matrix for several different weights. Save the kernel and burden, value and p-value for each
measurement in envir$pedgene_results.
Usage
DOpedgene(markers_arg, range_arg, envir = ENV)
Arguments
markers_arg |
a data.frame with the following 5 observations:
|
range_arg |
one row of a ranges_arg. The latter is a data frame of at least three integer columns. The columns indicate a range: a chromosome number, a start base pair value, and an end base pair value. |
envir |
'environment' containing SQLite database and other globals |
Value
None
Note
This function appends output to the data frame, envir$pedgene_results. It will print out the lines as they are generated if envir$verbose is TRUE. The data frame envir$pedgene_results is initialized by init_pedgene, and is appended to each time DOpedgene is run.
See Also
Examples
db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_pedgene(db)
ENV$verbose = TRUE
applyFnToRanges(DOpedgene, ENV$refRanges[50:60,], ENV$refIndices)
# donttestcheck: try this below if there is time
applyFnToGenes(DOpedgene, genes_arg = c("CEP104"))