Man pages for rqtl/qtl2geno
Treatment of Marker Genotypes for QTL Experiments
| 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 |
