basic_summaries | Basic summaries of a cross2 object |
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... |
calc_kinship | Calculate kinship matrix |
cbind.calc_genoprob | Join genotype probabilities for different chromosomes |
cbind.sim_geno | Join genotype imputations for different chromosomes |
cbind.viterbi | Join viterbi results for different chromosomes |
check_cross2 | Check a cross2 object |
chisq_colpairs | Chi-square test on all pairs of columns |
compare_geno | Compare individuals' genotype data |
compare_genoprob | Compare two sets of genotype probabilities |
convert2cross2 | Convert R/qtl cross object to new format |
count_xo | Count numbers of crossovers |
drop_markers | Drop markers from a cross2 object |
drop_nullmarkers | Drop markers with no genotype data |
est_map | Estimate genetic maps |
find_ibd_segments | Find IBD segments for a set of strains |
find_map_gaps | Find gaps in a genetic map |
find_marker | Find markers by chromosome position |
find_markerpos | Find positions of markers |
genoprob_to_alleleprob | Convert genotype probabilities to allele probabilities |
get_x_covar | Get X chromosome covariates |
guess_phase | Guess phase of imputed genotypes |
insert_pseudomarkers | Insert pseudomarkers into a marker map |
interp_genoprob | Interpolate genotype probabilities |
locate_xo | Locate crossovers |
map_to_grid | Subset a map to positions on a grid |
max_compare_geno | Find pair with most similar genotypes |
maxmarg | Find genotypes with maximum marginal probabilities |
n_missing | Count missing genotypes |
print.cross2 | Print a cross2 object |
probs_to_grid | Subset genotype probability array to pseudomarkers on a grid |
pull_markers | Drop all but a specified set of markers |
qtl2geno-package | qtl2geno: Treatment of Marker Genotypes for QTL Experiments |
rbind.calc_genoprob | Join genotype probabilities for different individuals |
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_csv | Read a csv file |
read_csv_numer | Read a csv file that has numeric columns |
read_pheno | Read phenotype data |
reduce_map_gaps | Reduce the lengths of gaps in a map |
reduce_markers | Reduce markers to a subset of more-evenly-spaced ones |
scale_kinship | Scale kinship matrix |
sim_geno | Simulate genotypes given observed marker data |
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 |
summary_compare_geno | Basic summary of compare_geno object |
summary.cross2 | Summary of cross2 object |
viterbi | Calculate most probable sequence of genotypes |
write_control_file | Write a control file for QTL data |
zip_datafiles | Zip a set of data files |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.