# Quantitative Trait Locus Mapping in Experimental Crosses

## Documentation for package ‘qtl2’ version 0.40

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L M N P Q R S T U V W X Z misc

## -- A --

add_threshold | Add thresholds to genome scan plot

## -- B --

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

## -- C --

c.scan1perm | Combine data from scan1perm objects
calc_entropy | Calculate entropy of genotype probability distribution
calc_errorlod | Calculate genotyping error LOD scores
calc_genoprob | Calculate conditional genotype probabilities
calc_geno_freq | Calculate genotype frequencies
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
CCaltcolors | Collaborative Cross colors
CCcolors | Collaborative Cross colors
CCorigcolors | Collaborative Cross colors
check_cross2 | Check a cross2 object
chisq_colpairs | Chi-square test on all pairs of columns
chr_lengths | Calculate chromosome lengths
chr_names | Basic summaries of a cross2 object
clean | Clean an object
clean.calc_genoprob | Clean genotype probabilities
clean.scan1 | Clean scan1 output
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
covar_names | Basic summaries of a cross2 object
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

## -- D --

decomp_kinship | Calculate eigen decomposition of kinship matrix
drop_markers | Drop markers from a cross2 object
drop_nullmarkers | Drop markers with no genotype data

## -- E --

est_herit | Estimate heritability with a linear mixed model
est_map | Estimate genetic maps

## -- F --

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
founders | Basic summaries of a cross2 object
fread_csv | Read a csv file
fread_csv_numer | Read a csv file that has numeric columns

## -- G --

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

## -- I --

index_snps | Create index of equivalent SNPs
ind_ids | Basic summaries of a cross2 object
ind_ids_covar | Basic summaries of a cross2 object
ind_ids_geno | Basic summaries of a cross2 object
ind_ids_gnp | Basic summaries of a cross2 object
ind_ids_pheno | Basic summaries of a cross2 object
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

## -- L --

locate_xo | Locate crossovers
lod_int | Calculate LOD support intervals

## -- M --

map_to_grid | Subset a map to positions on a grid
marker_names | Basic summaries of a cross2 object
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
max_compare_geno | Find pair with most similar genotypes
max_scan1 | Find position with maximum LOD score

## -- N --

n_chr | Basic summaries of a cross2 object
n_covar | Basic summaries of a cross2 object
n_founders | Basic summaries of a cross2 object
n_ind | Basic summaries of a cross2 object
n_ind_covar | Basic summaries of a cross2 object
n_ind_geno | Basic summaries of a cross2 object
n_ind_gnp | Basic summaries of a cross2 object
n_ind_pheno | Basic summaries of a cross2 object
n_mar | Basic summaries of a cross2 object
n_missing | Count missing genotypes
n_pheno | Basic summaries of a cross2 object
n_phenocovar | Basic summaries of a cross2 object
n_typed | Count missing genotypes

## -- P --

phenocovar_names | Basic summaries of a cross2 object
pheno_names | Basic summaries of a cross2 object
plot.calc_genoprob | Plot genotype probabilities for one individual on one chromosome.
plot.compare_geno | Plot of compare_geno object.
plot.scan1 | Plot a genome scan
plot.scan1coef | Plot QTL effects along chromosome
plot_ci | Effect plot with multiple CIs for different groups
plot_coef | Plot QTL effects along chromosome
plot_coefCC | 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.compare_geno | Basic summary of compare_geno 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

## -- Q --

qtl2version | Installed version of R/qtl2

## -- R --

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
replace_ids.calc_genoprob | Replace individual IDs
replace_ids.cross2 | Replace individual IDs
replace_ids.data.frame | Replace individual IDs
replace_ids.matrix | Replace individual IDs
replace_ids.sim_geno | Replace individual IDs
replace_ids.viterbi | Replace individual IDs

## -- S --

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.scan1 | Subset scan1 output
subset.sim_geno | Subsetting imputed genotypes
subset.viterbi | Subsetting Viterbi results
subset_scan1 | Subset scan1 output
summary.compare_geno | Basic summary of compare_geno object
summary.cross2 | Summary of cross2 object
summary.scan1perm | Summarize scan1perm results
summary_compare_geno | Basic summary of compare_geno object
summary_scan1perm | Summarize scan1perm results

## -- T --

top_snps | Create table of top snp associations
tot_mar | Basic summaries of a cross2 object

## -- U --

unsmooth_gmap | Unsmooth genetic map

## -- V --

viterbi | Calculate most probable sequence of genotypes

## -- W --

write_control_file | Write a control file for QTL data

## -- X --

xpos_scan1 | Get x-axis position for genomic location

## -- Z --

zip_datafiles | Zip a set of data files

## -- misc --

[.calc_genoprob | Subsetting genotype probabilities
[.cross2 | Subsetting data for a QTL experiment
[.sim_geno | Subsetting imputed genotypes
[.viterbi | Subsetting Viterbi results