Package: qtl2pleio 1.4.3.9000

qtl2pleio: Testing Pleiotropy in Multiparental Populations

We implement an adaptation of Jiang & Zeng's (1995) <https://www.genetics.org/content/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) <https://www.genetics.org/content/140/3/1111> 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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NEWS

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

Peer review:

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

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

On CRAN:

multiparental-populationsquantitative-geneticsquantitative-trait

28 exports 4 stars 1.59 score 34 dependencies 2 mentions 23 scripts 201 downloads

Last updated 3 years agofrom:d3406f399e. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 04 2024
R-4.5-win-x86_64NOTESep 04 2024
R-4.5-linux-x86_64NOTESep 04 2024
R-4.4-win-x86_64NOTESep 04 2024
R-4.4-mac-x86_64NOTESep 04 2024
R-4.4-mac-aarch64NOTESep 04 2024
R-4.3-win-x86_64OKSep 04 2024
R-4.3-mac-x86_64OKSep 04 2024
R-4.3-mac-aarch64OKSep 04 2024

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:clicolorspacedplyrfansifarvergemma2genericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcppRcppEigenrlangscalestibbletidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
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
qtl2pleio.qtl2pleio
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