# Testing Pleiotropy in Multiparental Populations

## Documentation for package ‘qtl2pleio’ version 1.4.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add_pmap | Add physical map contents to tibble
boot_pvl | Perform bootstrap sampling and calculate test statistic for each bootstrap sample
calc_Bhat | Calculate estimated allele effects, B matrix
calc_covs | Calculate Vg and Ve from d-variate phenotype and kinship
calc_invsqrt_mat | Calculate matrix inverse square root for a covariance matrix
calc_lrt_tib | Calculate a likelihood ratio test statistic from the output of scan_pvl()
calc_profile_lods | Calculate profile lods for all traits
calc_Sigma | Calculate the phenotypes covariance matrix Sigma
calc_sqrt_mat | Calculate matrix square root for a covariance matrix
check_identical | Check whether a vector, x, has all its entries equal to its first entry
check_missingness | Check for missingness in phenotypes or covariates
convert_to_scan1_output | Convert 'scan_multi_oneqtl' output of 'qtl2::scan1' output
find_pleio_peak_tib | Find the marker index corresponding to the peak of the pleiotropy trace in a tibble where the last column contains log likelihood values and the first d columns contain marker ids
fit1_pvl | Fit a model for a specified d-tuple of markers
get_effects | Extract founder allele effects at a single marker from output of qtl2::scan1coef
make_id2keep | Identify shared subject ids among all inputs: covariates, allele probabilities array, kinship, and phenotypes
plot_pvl | Plot tidied results of a pvl scan
prep_mytab | Prepare mytab object for use within scan_pvl R code
prep_X_list | Create a list of component X matrices for input to stagger_mats, to ultimately create design matrix
process_inputs | Process inputs to scan functions
qtl2pleio | qtl2pleio.
rcpp_calc_Bhat | Estimate allele effects matrix, B hat, with Rcpp functions
rcpp_calc_Bhat2 | Estimate allele effects matrix, B hat, with Rcpp functions
rcpp_log_dmvnorm2 | Calculate log likelihood for a multivariate normal
scan_multi_onechr | Perform multivariate, one-QTL model fitting for markers on one chromosome
scan_multi_oneqtl | Perform multivariate, one-QTL model fitting for markers on all chromosomes
scan_multi_oneqtl_perm | Permute the phenotypes matrix and then scan the genome. Record the genomewide greatest LOD score for each permuted data set.
scan_pvl | Perform model fitting for all ordered pairs of markers in a genomic region of interest
sim1 | Simulate a single multivariate data set consisting of n subjects and d phenotypes for each
subset_input | Subset an input object - allele probabilities array or phenotypes matrix or covariates matrix. Kinship has its own subset function
subset_kinship | Subset a kinship matrix to include only those subjects present in all inputs