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_hotspots           Calculate QTL hotspots
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.phasedgeno        Join phased genotype results 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_cistrans           cis-trans plot for eQTL results
plot_coef               Plot QTL effects along chromosome
plot_colorscale         Heat map color scale
plot_compare_geno       Plot of compare_geno object.
plot_genes              Plot gene locations for a genomic interval
plot_geno               Plot multiple individuals' genome-wide
                        genotypes
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_scan1_heatmap      Heat map of scan1 results with multiple traits
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.phasedgeno        Join phased geno results 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
scan1gen                General genome scan with a single-QTL model
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.phasedgeno       Subsetting phased genotype objects
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
