Man pages for qtl2
Quantitative Trait Locus Mapping in Experimental Crosses

add_thresholdAdd thresholds to genome scan plot
basic_summariesBasic summaries of a cross2 object
batch_colsBatch columns by pattern of missing values
batch_vecSplit vector into batches
bayes_intCalculate Bayes credible intervals
calc_entropyCalculate entropy of genotype probability distribution
calc_errorlodCalculate genotyping error LOD scores
calc_geno_freqCalculate genotype frequencies
calc_genoprobCalculate conditional genotype probabilities
calc_gridCalculate indicators of which marker/pseudomarker positions...
calc_hetCalculate heterozygosities
calc_kinshipCalculate kinship matrix
calc_raw_founder_mafCalculate founder minor allele frequencies from raw SNP...
calc_raw_geno_freqCalculate genotype frequencies from raw SNP genotypes
calc_raw_hetCalculate estimated heterozygosity from raw SNP genotypes
calc_raw_mafCalculate minor allele frequency from raw SNP genotypes
calc_sdpCalculate strain distribution pattern from SNP genotypes
cbind.calc_genoprobJoin genotype probabilities for different chromosomes
cbind_expandCombine matrices by columns, expanding and aligning rows
cbind.scan1Join genome scan results for different phenotypes.
cbind.scan1permCombine columns from multiple scan1 permutation results
cbind.sim_genoJoin genotype imputations for different chromosomes
cbind.viterbiJoin viterbi results for different chromosomes
CCcolorsCollaborative Cross colors
check_cross2Check a cross2 object
chisq_colpairsChi-square test on all pairs of columns
chr_lengthsCalculate chromosome lengths
cleanClean an object
clean_genoprobClean genotype probabilities
clean_scan1Clean scan1 output
compare_genoCompare individuals' genotype data
compare_genoprobCompare two sets of genotype probabilities
compare_mapsCompare two marker maps
convert2cross2Convert R/qtl cross object to new format
count_xoCount numbers of crossovers
create_gene_query_funcCreate a function to query genes
create_snpinfoCreate snp information table for a cross
create_variant_query_funcCreate a function to query variants
decomp_kinshipCalculate eigen decomposition of kinship matrix
drop_markersDrop markers from a cross2 object
drop_nullmarkersDrop markers with no genotype data
est_heritEstimate heritability with a linear mixed model
est_mapEstimate genetic maps
find_ibd_segmentsFind IBD segments for a set of strains
find_index_snpFind name of indexed snp
find_map_gapsFind gaps in a genetic map
find_markerFind markers by chromosome position
find_markerposFind positions of markers
find_peaksFind peaks in a set of LOD curves
fit1Fit single-QTL model at a single position
genoprob_to_alleleprobConvert genotype probabilities to allele probabilities
genoprob_to_snpprobConvert genotype probabilities to SNP probabilities
get_common_idsGet common set of IDs from objects
get_x_covarGet X chromosome covariates
guess_phaseGuess phase of imputed genotypes
index_snpsCreate index of equivalent SNPs
insert_pseudomarkersInsert pseudomarkers into a marker map
interp_genoprobInterpolate genotype probabilities
interp_mapInterpolate between maps
invert_sdpCalculate SNP genotype matrix from strain distribution...
locate_xoLocate crossovers
lod_intCalculate LOD support intervals
map_to_gridSubset a map to positions on a grid
mat2strataDefine strata based on rows of a matrix
max_compare_genoFind pair with most similar genotypes
maxlodOverall maximum LOD score
maxmargFind genotypes with maximum marginal probabilities
max_scan1Find position with maximum LOD score
n_missingCount missing genotypes
plot_coefPlot QTL effects along chromosome
plot_compare_genoPlot of compare_geno object.
plot_genesPlot gene locations for a genomic interval
plot_genoprobPlot genotype probabilities for one individual on one...
plot_genoprobcompPlot comparison of two sets of genotype probabilities
plot_lodpeaksPlot LOD scores vs QTL peak locations
plot_onegenoPlot one individual's genome-wide genotypes
plot_peaksPlot QTL peak locations
plot_pxgPlot phenotype vs genotype
plot_scan1Plot a genome scan
plot_sdpplot strain distribution patterns for SNPs
plot_snpassoPlot SNP associations
predict_snpgenoPredict SNP genotypes
print.cross2Print a cross2 object
print.summary.scan1permPrint summary of scan1perm permutations
probs_to_gridSubset genotype probability array to pseudomarkers on a grid
pull_genoprobintPull genotype probabilities for an interval
pull_genoprobposPull genotype probabilities for a particular position
pull_markersDrop all but a specified set of markers
qtl2-internalInternal functions
qtl2-packageqtl2: Quantitative Trait Locus Mapping in Experimental...
qtl2versionInstalled version of R/qtl2
rbind.calc_genoprobJoin genotype probabilities for different individuals
rbind.scan1Join genome scan results for different chromosomes.
rbind.scan1permCombine data from scan1perm objects
rbind.sim_genoJoin genotype imputations for different individuals
rbind.viterbiJoin Viterbi results for different individuals
read_cross2Read QTL data from files
read_csvRead a csv file
read_csv_numerRead a csv file that has numeric columns
read_phenoRead phenotype data
recode_snpsRecode SNPs by major allele
reduce_map_gapsReduce the lengths of gaps in a map
reduce_markersReduce markers to a subset of more-evenly-spaced ones
replace_idsReplace individual IDs
scale_kinshipScale kinship matrix
scan1Genome scan with a single-QTL model
scan1blupCalculate BLUPs of QTL effects in scan along one chromosome
scan1coefCalculate QTL effects in scan along one chromosome
scan1maxMaximum LOD score from genome scan with a single-QTL model
scan1permPermutation test for genome scan with a single-QTL model
scan1snpsSingle-QTL genome scan at imputed SNPs
sdp2charConvert strain distribution patterns to character strings
sim_genoSimulate genotypes given observed marker data
subset.calc_genoprobSubsetting genotype probabilities
subset.cross2Subsetting data for a QTL experiment
subset_scan1Subset scan1 output
subset.sim_genoSubsetting imputed genotypes
subset.viterbiSubsetting Viterbi results
summary_compare_genoBasic summary of compare_geno object
summary.cross2Summary of cross2 object
summary_scan1permSummarize scan1perm results
top_snpsCreate table of top snp associations
viterbiCalculate most probable sequence of genotypes
write_control_fileWrite a control file for QTL data
xpos_scan1Get x-axis position for genomic location
zip_datafilesZip a set of data files
qtl2 documentation built on Oct. 18, 2021, 1:06 a.m.