CCcolors                Collaborative Cross colors
add_threshold           Add thresholds to genome scan plot
basic_summaries         Basic summaries of a cross2 object
batch_cols              Batch columns by pattern of missing values
batch_vec               Split vector into batches
bayes_int               Calculate Bayes credible intervals
calc_entropy            Calculate entropy of genotype probability
                        distribution
calc_errorlod           Calculate genotyping error LOD scores
calc_geno_freq          Calculate genotype frequencies
calc_genoprob           Calculate conditional genotype probabilities
calc_grid               Calculate indicators of which
                        marker/pseudomarker positions are along a fixed
                        grid
calc_het                Calculate heterozygosities
calc_kinship            Calculate kinship matrix
calc_raw_founder_maf    Calculate founder minor allele frequencies from
                        raw SNP genotypes
calc_raw_geno_freq      Calculate genotype frequencies from raw SNP
                        genotypes
calc_raw_het            Calculate estimated heterozygosity from raw SNP
                        genotypes
calc_raw_maf            Calculate minor allele frequency from raw SNP
                        genotypes
calc_sdp                Calculate strain distribution pattern from SNP
                        genotypes
cbind.calc_genoprob     Join genotype probabilities for different
                        chromosomes
cbind.scan1             Join genome scan results for different
                        phenotypes.
cbind.scan1perm         Combine columns from multiple scan1 permutation
                        results
cbind.sim_geno          Join genotype imputations for different
                        chromosomes
cbind.viterbi           Join viterbi results for different chromosomes
cbind_expand            Combine matrices by columns, expanding and
                        aligning rows
check_cross2            Check a cross2 object
chisq_colpairs          Chi-square test on all pairs of columns
chr_lengths             Calculate chromosome lengths
clean                   Clean an object
clean_genoprob          Clean genotype probabilities
clean_scan1             Clean scan1 output
compare_founder_geno    Compare founders genotype data
compare_geno            Compare individuals' genotype data
compare_genoprob        Compare two sets of genotype probabilities
compare_maps            Compare two marker maps
convert2cross2          Convert R/qtl cross object to new format
count_xo                Count numbers of crossovers
create_gene_query_func
                        Create a function to query genes
create_snpinfo          Create snp information table for a cross
create_variant_query_func
                        Create a function to query variants
decomp_kinship          Calculate eigen decomposition of kinship matrix
drop_markers            Drop markers from a cross2 object
drop_nullmarkers        Drop markers with no genotype data
est_herit               Estimate heritability with a linear mixed model
est_map                 Estimate genetic maps
find_dup_markers        Find markers with identical genotype data
find_ibd_segments       Find IBD segments for a set of strains
find_index_snp          Find name of indexed snp
find_map_gaps           Find gaps in a genetic map
find_marker             Find markers by chromosome position
find_markerpos          Find positions of markers
find_peaks              Find peaks in a set of LOD curves
fit1                    Fit single-QTL model at a single position
fread_csv               Read a csv file
fread_csv_numer         Read a csv file that has numeric columns
genoprob_to_alleleprob
                        Convert genotype probabilities to allele
                        probabilities
genoprob_to_snpprob     Convert genotype probabilities to SNP
                        probabilities
get_common_ids          Get common set of IDs from objects
get_x_covar             Get X chromosome covariates
guess_phase             Guess phase of imputed genotypes
index_snps              Create index of equivalent SNPs
insert_pseudomarkers    Insert pseudomarkers into a marker map
interp_genoprob         Interpolate genotype probabilities
interp_map              Interpolate between maps
invert_sdp              Calculate SNP genotype matrix from strain
                        distribution patterns
locate_xo               Locate crossovers
lod_int                 Calculate LOD support intervals
map_to_grid             Subset a map to positions on a grid
mat2strata              Define strata based on rows of a matrix
max_compare_geno        Find pair with most similar genotypes
max_scan1               Find position with maximum LOD score
maxlod                  Overall maximum LOD score
maxmarg                 Find genotypes with maximum marginal
                        probabilities
n_missing               Count missing genotypes
plot_ci                 Effect plot with multiple CIs for different
                        groups
plot_coef               Plot QTL effects along chromosome
plot_compare_geno       Plot of compare_geno object.
plot_genes              Plot gene locations for a genomic interval
plot_genoprob           Plot genotype probabilities for one individual
                        on one chromosome.
plot_genoprobcomp       Plot comparison of two sets of genotype
                        probabilities
plot_lodpeaks           Plot LOD scores vs QTL peak locations
plot_onegeno            Plot one individual's genome-wide genotypes
plot_peaks              Plot QTL peak locations
plot_pxg                Plot phenotype vs genotype
plot_scan1              Plot a genome scan
plot_sdp                plot strain distribution patterns for SNPs
plot_snpasso            Plot SNP associations
predict_snpgeno         Predict SNP genotypes
print.cross2            Print a cross2 object
print.summary.scan1perm
                        Print summary of scan1perm permutations
probs_to_grid           Subset genotype probability array to
                        pseudomarkers on a grid
pull_genoprobint        Pull genotype probabilities for an interval
pull_genoprobpos        Pull genotype probabilities for a particular
                        position
pull_markers            Drop all but a specified set of markers
qtl2version             Installed version of R/qtl2
rbind.calc_genoprob     Join genotype probabilities for different
                        individuals
rbind.scan1             Join genome scan results for different
                        chromosomes.
rbind.scan1perm         Combine data from scan1perm objects
rbind.sim_geno          Join genotype imputations for different
                        individuals
rbind.viterbi           Join Viterbi results for different individuals
read_cross2             Read QTL data from files
read_pheno              Read phenotype data
recode_snps             Recode SNPs by major allele
reduce_map_gaps         Reduce the lengths of gaps in a map
reduce_markers          Reduce markers to a subset of
                        more-evenly-spaced ones
replace_ids             Replace individual IDs
scale_kinship           Scale kinship matrix
scan1                   Genome scan with a single-QTL model
scan1blup               Calculate BLUPs of QTL effects in scan along
                        one chromosome
scan1coef               Calculate QTL effects in scan along one
                        chromosome
scan1max                Maximum LOD score from genome scan with a
                        single-QTL model
scan1perm               Permutation test for genome scan with a
                        single-QTL model
scan1snps               Single-QTL genome scan at imputed SNPs
sdp2char                Convert strain distribution patterns to
                        character strings
sim_geno                Simulate genotypes given observed marker data
smooth_gmap             Smooth genetic map
subset.calc_genoprob    Subsetting genotype probabilities
subset.cross2           Subsetting data for a QTL experiment
subset.sim_geno         Subsetting imputed genotypes
subset.viterbi          Subsetting Viterbi results
subset_scan1            Subset scan1 output
summary.cross2          Summary of cross2 object
summary_compare_geno    Basic summary of compare_geno object
summary_scan1perm       Summarize scan1perm results
top_snps                Create table of top snp associations
unsmooth_gmap           Unsmooth genetic map
viterbi                 Calculate most probable sequence of genotypes
write_control_file      Write a control file for QTL data
xpos_scan1              Get x-axis position for genomic location
zip_datafiles           Zip a set of data files
