Package: qtl2pleio 1.4.4

qtl2pleio: Testing Pleiotropy in Multiparental Populations

We implement an adaptation of Jiang & Zeng's (1995) <doi:10.1093/genetics/140.3.1111> likelihood ratio test for testing the null hypothesis of pleiotropy against the alternative hypothesis, two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995) and that in Tian et al. (2016) <doi:10.1534/genetics.115.183624> in that our test accommodates multiparental populations.

Authors:Frederick J Boehm [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
qtl2pleio/json (API)

# Install 'qtl2pleio' in R:
install.packages('qtl2pleio', repos = c('https://fboehm.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fboehm/qtl2pleio/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

multiparental-populationsquantitative-geneticsquantitative-traitcpp

5.19 score 6 stars 29 scripts 496 downloads 2 mentions 28 exports 31 dependencies

Last updated from:d1dfcf7ab6. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK168
linux-devel-x86_64OK242
source / vignettesOK222
linux-release-arm64OK158
linux-release-x86_64OK238
macos-release-arm64OK137
macos-release-x86_64OK346
macos-oldrel-arm64OK139
macos-oldrel-x86_64OK343
windows-devel-arm64OK435
windows-devel-x86_64OK209
windows-release-arm64OK393
windows-release-x86_64OK168
windows-oldrel-x86_64OK168
wasm-releaseOK152

Exports:%>%add_pmapboot_pvlcalc_Bhatcalc_covscalc_lrt_tibcalc_profile_lodscalc_Sigmacheck_identicalcheck_missingnessconvert_to_scan1_outputfind_pleio_peak_tibfit1_pvlget_effectsmake_id2keepplot_pvlprep_mytabprep_X_listrcpp_calc_Bhatrcpp_calc_Bhat2rcpp_log_dmvnorm2scan_multi_onechrscan_multi_oneqtlscan_multi_oneqtl_permscan_pvlsim1subset_inputsubset_kinship

Dependencies:clicpp11dplyrfarvergemma2genericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixpillarpkgconfigR6RColorBrewerRcppRcppEigenrlangS7scalestibbletidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
qtl2pleio.qtl2pleio-package qtl2pleio
Add physical map contents to tibbleadd_pmap
Perform bootstrap sampling and calculate test statistic for each bootstrap sampleboot_pvl
Calculate estimated allele effects, B matrixcalc_Bhat
Calculate Vg and Ve from d-variate phenotype and kinshipcalc_covs
Calculate matrix inverse square root for a covariance matrixcalc_invsqrt_mat
Calculate a likelihood ratio test statistic from the output of scan_pvl()calc_lrt_tib
Calculate profile lods for all traitscalc_profile_lods
Calculate the phenotypes covariance matrix Sigmacalc_Sigma
Calculate matrix square root for a covariance matrixcalc_sqrt_mat
Check whether a vector, x, has all its entries equal to its first entrycheck_identical
Check for missingness in phenotypes or covariatescheck_missingness
Convert `scan_multi_oneqtl` output of `qtl2::scan1` outputconvert_to_scan1_output
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 idsfind_pleio_peak_tib
Fit a model for a specified d-tuple of markersfit1_pvl
Extract founder allele effects at a single marker from output of qtl2::scan1coefget_effects
Identify shared subject ids among all inputs: covariates, allele probabilities array, kinship, and phenotypesmake_id2keep
Plot tidied results of a pvl scanplot_pvl
Prepare mytab object for use within scan_pvl R codeprep_mytab
Create a list of component X matrices for input to stagger_mats, to ultimately create design matrixprep_X_list
Process inputs to scan functionsprocess_inputs
Estimate allele effects matrix, B hat, with Rcpp functionsrcpp_calc_Bhat
Estimate allele effects matrix, B hat, with Rcpp functionsrcpp_calc_Bhat2
Calculate log likelihood for a multivariate normalrcpp_log_dmvnorm2
Perform multivariate, one-QTL model fitting for markers on one chromosomescan_multi_onechr
Perform multivariate, one-QTL model fitting for markers on all chromosomesscan_multi_oneqtl
Permute the phenotypes matrix and then scan the genome. Record the genomewide greatest LOD score for each permuted data set.scan_multi_oneqtl_perm
Perform model fitting for all ordered pairs of markers in a genomic region of interestscan_pvl
Simulate a single multivariate data set consisting of n subjects and d phenotypes for eachsim1
Subset an input object - allele probabilities array or phenotypes matrix or covariates matrix. Kinship has its own subset functionsubset_input
Subset a kinship matrix to include only those subjects present in all inputssubset_kinship