Michael G. Campana, 2018-2024
Smithsonian Conservation Biology Institute
R code to perform bootstrapping analysis and generate triangular kinship matrices from SNPRelate (Zheng et al. 2012. Bioinformatics. 28: 3326-3328.) Identity-by-Descent results.
The software is made available under the Smithsonian Institution terms of use.
In the terminal:
git clone https://github.com/campanam/kinshipUtils
In your R environment:
source("/path/to/kinshipUtils.R")
bootstrap.kinship is a wrapper function around snpgdsLDpruning, snpgdsIBDMoM and snpgdsIBDMLE. Unless specified below, all parameters correspond to the parameters in those SNPRelate functions.
ibdmethod: "MoM" specifies to use the snpgdsIBDMoM function. "MLE" specifies to use the snpgdsIBDMLE function.
mlemethod: Method to perform MLE if snpgdsIBDMLE specified. Passes the value to the method parameter of snpgdsIBDMLE.
resample: Number of bootstrap replicates. Default is 100.
ldmethod: Method to perform LD pruning. Passes the value to the method parameter of snpgdsLDpruning.
bootstrap.kinship generates a table with the following columns:
Sample1 Sample2 KinshipRep1 ... KinshipRepN MeanKinship StandardError LowCI HighCI
MeanKinship and StandardError list the mean kinship estimate and the corresponding standard errors for each sample pair. LowCI and HighCI give the lower and upper bounds of the 95% Confidence interval respectively.
write.kinship.matrix generates triangular matrices for each sample pair from the bootstrap.kinship results table. Results are written as text files in the current working directory.
x: bootstrap.kinship results file to process.
meanfile: Name of output file to include only mean kinship values.
cifile: Name of output file to include mean and confidence interval values.
sep: Separator for values. Default is a comma (for CSV).
digits: Number of digits for values rounding. Default is 3.
Please cite:
Cortes-Rodriguez N, Campana MG, Berry L et al. (2019) Population genomics and structure of the critically endangered Mariana crow (Corvus kubaryi). Genes, 10, 187. doi: 10.3390/genes10030187.