setSNPs {pedtools} | R Documentation |
Attach SNP loci to a pedigree
Description
Create and attach a list of empty SNP markers with specified position and allele frequencies.
Usage
setSNPs(x, snpData)
Arguments
x |
A |
snpData |
A data frame with 6 columns. See Details. |
Details
The data frame snpData
should contain the following columns, in order:
-
CHROM
: Chromosome (character) -
MARKER
: Marker name (character) -
MB
: Physical position in megabases (numeric) -
A1
: First allele (single-letter character) -
A2
: Second allele (single-letter character) -
FREQ1
: Allele frequency ofA1
(number in[0,1]
)
The actual column names do not matter.
Each column must be of the stated type, or coercible to it. (For example,
CHROM
, A1
and A2
may be given as numbers, but will be internally
converted to characters.)
Value
A copy of x
with the indicated SNP markers attached.
Examples
snps = data.frame(
CHROM = 1:2,
MARKER = c("M1", "M2"),
MB = c(1.23, 2.34),
A1 = c("A", "G"),
A2 = c("C", "C"),
FREQ1 = c(0.7, 0.12))
x = setSNPs(nuclearPed(), snpData = snps)
# Inspect the results:
getMap(x)
getFreqDatabase(x)
[Package pedtools version 2.7.0 Index]