- qtl: Tools for Analyzing QTL Experiments
- scanonevar.meanperm: Permutation test for mean effect in scanonevar
Permutation test for mean effect in scanonevar
Executes permutations of the genotypes in the mean-effect part of scanonevar
An object of class
Column number in the phenotype matrix which should be used as the phenotype. This must be a single value (integer index or phenotype name) or a numeric vector of phenotype values, in which case it must have the length equal to the number of individuals in the cross, and there must be either non-integers or values < 1 or > no. phenotypes; this last case may be useful for studying transformations.
Numeric matrix with covariates affecting the mean.
Numeric matrix with covariates affecting the variances.
Maximum number of iterations in the algorithm to fit the model at a given position.
Tolerance for convergence.
Numeric vector of length one indicates the number of permutations to execute.
Numeric vector of length one indicates the random seed to start the permutations.
A vector of length
n.mean.perm of the maximum negative log10 p-value that resulted from each permutation.
- add.cim.covar: Indicate marker covariates from composite interval mapping
- addcovarint: Add QTL x covariate interaction to a multiple-QTL model
- addint: Add pairwise interaction to a multiple-QTL model
- addloctocross: Add phenotype location into a cross object
- addmarker: Add a marker to a cross
- addpair: Scan for an additional pair of QTL in a multiple-QTL model
- addqtl: Scan for an additional QTL in a multiple-QTL model
- add.threshold: Add significance threshold to plot
- addtoqtl: Add to a qtl object
- allchrsplits: Test all possible splits of a chromosome into two pieces
- argmax.geno: Reconstruct underlying genotypes
- arithscan: Arithmetic operators for scanone and scantwo results
- arithscanperm: Arithmetic Operators for permutation results
- a.starting.point: Introductory comments on R/qtl
- badorder: An intercross with misplaced markers
- bayesint: Bayesian credible interval
- bristle3: Data on bristle number in Drosophila
- bristleX: Data on bristle number in Drosophila
- calc.errorlod: Identify likely genotyping errors
- calc.genoprob: Calculate conditional genotype probabilities
- calc.penalties: Calculate LOD penalties
- cbind.scanoneperm: Combine columns from multiple scanone permutation results
- cbind.scantwoperm: Combine scantwo permutations by column
- c.cross: Combine data for QTL experiments
- checkAlleles: Identify markers with switched alleles
- chrlen: Chromosome lengths in QTL experiment
- chrnames: Pull out the chromosome names from a cross
- cim: Composite interval mapping
- clean.cross: Remove derived data
- cleanGeno: Delete genotypes that are possibly in error
- clean.scantwo: Clean up scantwo output
- comparecrosses: Compare two cross objects
- comparegeno: Compare individuals' genotype data
- compareorder: Compare two orderings of markers on a chromosome
- condense.scantwo: Condense the output from a 2-d genome scan
- convert2riself: Convert a cross to RIL by selfing
- convert2risib: Convert a cross to RIL by sib mating
- convert2sa: Convert a sex-specific map to a sex-averaged one
- convert.map: Change map function for a genetic map
- convert.scanone: Convert output from scanone for R/qtl version 0.98
- convert.scantwo: Convert output from scantwo for R/qtl version 1.03 and...
- countXO: Count number of obligate crossovers for each individual
- c.scanone: Combine columns from multiple scanone results
- c.scanoneperm: Combine data from scanone permutations
- c.scantwo: Combine columns from multiple scantwo results
- c.scantwoperm: Combine data from scantwo permutations
- drop.dupmarkers: Drop duplicate markers
- dropfromqtl: Drop a QTL from a qtl object
- drop.markers: Drop a set of markers
- drop.nullmarkers: Drop markers without any genotype data
- droponemarker: Drop one marker at a time and determine effect on genetic map
- effectplot: Plot phenotype means against genotypes at one or two markers
- effectscan: Plot estimated QTL effects across the whole genome
- est.map: Estimate genetic maps
- est.rf: Estimate pairwise recombination fractions
- fake.4way: Simulated data for a 4-way cross
- fake.bc: Simulated data for a backcross
- fake.f2: Simulated data for an F2 intercross
- fill.geno: Fill holes in genotype data
- findDupMarkers: Find markers with identical genotype data
- find.flanking: Find flanking markers for a specified position
- find.marker: Find marker closest to a specified position
- findmarkerindex: Determine the numeric index for a marker
- find.markerpos: Find position of a marker
- find.pheno: Find column number for a particular phenotype
- find.pseudomarker: Find the pseudomarker closest to a specified position
- fitqtl: Fit a multiple-QTL model
- fitstahl: Fit Stahl interference model
- flip.order: Flip the orders of markers on a set of chromosomes
- formLinkageGroups: Partition markers into linkage groups
- formMarkerCovar: Create matrix of marker covariates for QTL analysis
- geno.crosstab: Create table of two-locus genotypes
- geno.image: Plot grid of genotype data
- geno.table: Create table of genotype distributions
- getid: Pull out the individual identifiers from a cross
- groupclusteredheatmap: Retrieving groups of traits after clustering
- hyper: Data on hypertension
- inferFounderHap: Crude reconstruction of founder haplotypes in multi-parent...
- inferredpartitions: Identify inferred partitions in mapping QTL to a phylogenetic...
- interpPositions: Interpolate positions from one map to another
- jittermap: Jitter marker positions in a genetic map
- listeria: Data on Listeria monocytogenes susceptibility
- locateXO: Estimate locations of crossovers
- locations: Genetic locations of traits for the multitrait dataset
- lodint: LOD support interval
- makeqtl: Make a qtl object
- map10: An example genetic map
- map2table: Convert genetic map from list to table.
- mapthis: Simulated data for illustrating genetic map construction
- markerlrt: General likelihood ratio test for association between marker...
- markernames: Pull out the marker names from a cross
- max.scanone: Maximum peak in genome scan
- max.scanPhyloQTL: Maximum peak in genome scan to map a QTL to a phylogenetic...
- max.scantwo: Maximum peak in two-dimensional genome scan
- movemarker: Move a marker to a new chromosome
- MQM: Introduction to Multiple QTL Model (MQM) mapping
- mqmaugment: MQM augmentation
- mqmautocofactors: Automatic setting of cofactors, taking marker density into...
- mqmextractmarkers: MQM marker extraction
- mqmfind.marker: Fetch significant markers after permutation analysis
- mqmgetmodel: Retrieve the QTL model used in mapping from the results of an...
- mqmpermutation: Estimate QTL LOD score significance using permutations or...
- mqmplotcircle: Circular genome plot for MQM
- mqmplotcistrans: cis-trans plot
- mqmplotclusteredheatmap: Plot clustered heatmap of MQM scan on multiple phenotypes
- mqmplotcofactors: Plot cofactors on the genetic map
- mqmplotdirectedqtl: Plot LOD*Effect curves of a multiple-QTL model
- mqmplotheatmap: Heatmap of a genome of MQM scan on multiple phenotypes
- mqmplotmultitrait: Plot the results from a genomescan using a multiple-QTL model...
- mqmplotpermutations: Plot results from mqmpermutation
- mqmplotsingletrait: Plot LOD curves of a multiple-QTL model
- mqmprocesspermutation: Convert mqmmulti objects into a scanoneperm object
- mqmscan: Genome scan with a multiple QTL model (MQM)
- mqmscanall: Parallelized MQM on multiple phenotypes in a cross object
- mqmscanfdr: Estimate FDR for multiple trait QTL analysis
- mqmsetcofactors: Set cofactors at fixed intervals, to be used with MQM
- mqmtestnormal: Shapiro normality test used for MQM
- multitrait: Example Cross object from R/QTL with multiple traits
- nchr: Determine the number of chromosomes
- nind: Determine the number of individuals QTL experiment
- nmar: Determine the numbers of markers on each chromosome
- nmissing: Number of missing genotypes
- nphe: Determine the number of phenotypes QTL experiment
- nqrank: Transform a vector of quantitative values to the...
- nqtl: Determine the number of QTL in a QTL object
- ntyped: Number of genotypes
- nullmarkers: Identify markers without any genotype data
- orderMarkers: Find an initial order for markers within chromosomes
- phenames: Pull out the phenotypes names from a cross
- pickMarkerSubset: Identify the largest subset of markers that are some distance...
- plot.cross: Plot various features of a cross object
- plot.errorlod: Plot grid of error LOD values
- plot.geno: Plot observed genotypes, flagging likely errors
- plot.info: Plot the proportion of missing genotype information
- plotLodProfile: Plot 1-d LOD profiles for a multiple QTL model
- plot.map: Plot genetic map
- plot.missing: Plot grid of missing genotypes
- plotModel: Plot a QTL model
- plot.pheno: Plot a phenotype distribution
- plot.pxg: Plot phenotypes versus marker genotypes
- plot.qtl: Plot QTL locations
- plot.rf: Plot recombination fractions
- plot.rfmatrix: Plot recombination fractions or LOD scores for a single...
- plot.scanone: Plot LOD curves
- plot.scanoneboot: Plot results of bootstrap for QTL position
- plot.scanoneperm: Plot permutation results for a single-QTL genome scan
- plot.scanPhyloQTL: Plot LOD curves from single-QTL scan to map QTL to a...
- plot.scantwo: Plot LOD scores for a two-dimensional genome scan
- plot.scantwoperm: Plot permutation results for a 2d, 2-QTL genome scan
- pull.argmaxgeno: Pull out the results of the Viterbi algorithm from a cross
- pull.draws: Pull out the genotype imputations from a cross
- pull.geno: Pull out the genotype data from a cross
- pull.genoprob: Pull out the genotype probabilities from a cross
- pull.map: Pull out the genetic map from a cross
- pull.markers: Drop all but a selected set of markers
- pull.pheno: Pull out phenotype data from a cross
- pull.rf: Pull out recombination fractions or LOD scores from a cross...
- qtl-internal: Internal qtl functions
- qtlversion: Installed version of R/qtl
- read.cross: Read data for a QTL experiment
- readMWril: Read data for 4- or 8-way RIL
- reduce2grid: Reduce to a grid of pseudomarkers.
- refineqtl: Refine the positions of QTL
- reorderqtl: Reorder the QTL in a qtl object
- replace.map: Replace the genetic map of a cross
- replacemap.scanone: Replace the genetic map in QTL mapping results with an...
- replacemap.scantwo: Replace the genetic map in QTL mapping results with an...
- replaceqtl: Replace a QTL in a qtl object with a different position
- rescalemap: Rescale genetic maps
- ripple: Compare marker orders
- scanone: Genome scan with a single QTL model
- scanoneboot: Bootstrap to get interval estimate of QTL location
- scanonevar: Genome scan for QTL affecting mean and/or variance
- scanonevar.meanperm: Permutation test for mean effect in scanonevar
- scanonevar.varperm: Permutation test for variance effect in scanonevar
- scanPhyloQTL: Single-QTL genome scan to map QTL to a phylogenetic tree
- scanqtl: General QTL scan
- scantwo: Two-dimensional genome scan with a two-QTL model
- scantwopermhk: Permutation test for 2d genome scan by Haley-Knott regression
- shiftmap: Shift starting points in genetic maps
- sim.cross: Simulate a QTL experiment
- simFounderSnps: Simulate founder SNPs for a multiple-strain RIL
- sim.geno: Simulate genotypes given observed marker data
- sim.map: Simulate a genetic map
- simPhyloQTL: Simulate a set of intercrosses for a single diallelic QTL
- simulateMissingData: Simulates missing genotype data
- stepwiseqtl: Stepwise selection for multiple QTL
- strip.partials: Strip partially informative genotypes
- subset.cross: Subsetting data for QTL experiment
- subset.map: Subsetting chromosomes for a genetic map
- subset.scanone: Subsetting the results of a genome scan
- subset.scanoneperm: Subsetting permutation test results
- subset.scantwo: Subsetting the results of a 2-d genome scan
- subset.scantwoperm: Subsetting two-dimensional permutation test results
- summary.cross: Print summary of QTL experiment
- summary.fitqtl: Summary of fit of qtl model
- summary.map: Print summary of a genetic map
- summary.qtl: Print summary of a QTL object
- summary.ripple: Print summary of ripple results
- summary.scanone: Summarize the results of a genome scans
- summary.scanoneboot: Bootstrap confidence interval for QTL location
- summary.scanoneperm: LOD thresholds from scanone permutation results
- summary.scanPhyloQTL: Summarize the results a genome scan to map a QTL to a...
- summary.scantwo: Summarize the results of a two-dimensional genome scan
- summary.scantwo.old: Summarize the results of a two-dimensional genome scan
- summary.scantwoperm: LOD thresholds from scantwo permutation results
- switchAlleles: Switch alleles at selected markers
- switch.order: Switch the order of markers on a chromosome
- table2map: Convert a table of marker positions to a map object.
- top.errorlod: List genotypes with large error LOD scores
- totmar: Determine the total number of markers
- transformPheno: Transformation of the phenotypes in a cross object
- tryallpositions: Test all possible positions for a marker
- typingGap: Maximum distance between genotyped markers
- write.cross: Write data for a QTL experiment to a file
- xaxisloc.scanone: Get x-axis locations in scanone plot