qtl2pleio1.4.3 package

Add physical map contents to tibble

Perform bootstrap sampling and calculate test statistic for each boots...

Calculate estimated allele effects, B matrix

Calculate Vg and Ve from d-variate phenotype and kinship

Calculate matrix inverse square root for a covariance matrix

Calculate a likelihood ratio test statistic from the output of scan_pv...

Calculate profile lods for all traits

Calculate the phenotypes covariance matrix Sigma

Calculate matrix square root for a covariance matrix

Check whether a vector, x, has all its entries equal to its first entr...

Check for missingness in phenotypes or covariates

Convert scan_multi_oneqtl output of qtl2::scan1 output

Find the marker index corresponding to the peak of the pleiotropy trac...

Fit a model for a specified d-tuple of markers

Extract founder allele effects at a single marker from output of qtl2:...

Identify shared subject ids among all inputs: covariates, allele proba...

Pipe operator

Plot tidied results of a pvl scan

Prepare mytab object for use within scan_pvl R code

Create a list of component X matrices for input to stagger_mats, to ul...

Process inputs to scan functions

qtl2pleio.

Estimate allele effects matrix, B hat, with Rcpp functions

Estimate allele effects matrix, B hat, with Rcpp functions

Calculate log likelihood for a multivariate normal

Perform multivariate, one-QTL model fitting for markers on one chromos...

Perform multivariate, one-QTL model fitting for markers on all chromos...

Permute the phenotypes matrix and then scan the genome. Record the gen...

Perform model fitting for all ordered pairs of markers in a genomic re...

Simulate a single multivariate data set consisting of n subjects and d...

Subset an input object - allele probabilities array or phenotypes matr...

Subset a kinship matrix to include only those subjects present in all ...