Man pages for qtl2pleio
Testing Pleiotropy in Multiparental Populations

add_pmapAdd physical map contents to tibble
boot_pvlPerform bootstrap sampling and calculate test statistics for...
calc_BhatCalculate estimated allele effects, B matrix
calc_covsCalculate Vg and Ve from d-variate phenotype and kinship
calc_invsqrt_matCalculate matrix inverse square root for a covariance matrix
calc_lrt_tibCalculate a likelihood ratio test statistic from the output...
calc_profile_lodsCalculate profile lods for all traits
calc_SigmaCalculate the phenotypes covariance matrix Sigma
calc_sqrt_matCalculate matrix square root for a covariance matrix
check_identicalCheck whether a vector, x, has all its entries equal to its...
check_missingnessCheck for missingness in phenotypes or covariates
find_pleio_peak_tibFind the marker index corresponding to the peak of the...
fit1_pvlFit a model for a specified d-tuple of markers
get_effectsExtract founder allele effects at a single marker from output...
make_id2keepIdentify shared subject ids among all inputs: covariates,...
pipePipe operator
plot_pvlPlot tidied results of a pvl scan
prep_mytabPrepare mytab object for use within scan_pvl R code
prep_X_listCreate a list of component X matrices for input to...
qtl2pleioqtl2pleio.
rcpp_calc_BhatEstimate allele effects matrix, B hat, with Rcpp functions
rcpp_calc_Bhat2Estimate allele effects matrix, B hat, with Rcpp functions
rcpp_log_dmvnorm2Calculate log likelihood for a multivariate normal
scan_pvlPerform model fitting for all ordered pairs of markers in a...
sim1Simulate a single data set consisting of n subjects and 2...
subset_inputSubset an input object - allele probabilities array or...
subset_kinshipSubset a kinship matrix to include only those subjects...
qtl2pleio documentation built on Nov. 5, 2019, 5:06 p.m.