R package encapsulating methods presented in Estimation of genome-wide and locus-specific breed composition in pigs published in Translational Animal Science (TAS). Note that functions contained in this package have been tested and used on Linux and Mac platforms only.
breedTools can be used to estimate breed composition from DNA microarray data and has been applied to the estimation of pig breed composition and purity.
The methods in this package require a set of reference data (genotypes).
NOTE: Several functions in breedTools
rely on another package,
snpTools
.
First ensure devtools
is installed,
then install snpTools
with:
devtools::install_github("funkhou9/snpTools")
then install breedTools
with:
devtools::install_github("funkhou9/breedTools")
attaching the breedTools
package with:
library(breedTools)
will allow access to reference pig datasets.
Key functions include:
solve_composition()
to estimate genome-wide breed composition (GWBC) for a
set of animals, given a reference panel.
solve_KBP()
to estimate local, KIT-based breed probabilities (KBP) for a
set of animals, based on looking at haplotypes within the KIT region on
chromosome 8.
screen_purity()
combines GWBC and KBP methods and provides a full report
for a set of animals.
build_KBP()
is used to build a new reference panel for KBP estimation.
Using this function requires installation of FImpute.
Note that the path
argument is used to specify the location of the FImpute
binary if FImpute is not on your PATH.
allele_freq()
is used to build a new reference panel for GWBC estimation.
Note other functions in snpTools
such as snpTools::filter_geno()
, which
filters out SNPs based on MAF.
Example GWBC and KBP reference panels GWBC_ref_A
, GWBC_ref_B
, KBP_ref_A
,
and KBP_ref_B
can be loaded with, for example:
data("GWBC_ref_A")
Note that GWBC_ref_A
and KBP_ref_A
are used to generate the results in the
TAS paper.
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