Man pages for rqtl/qtl2scan
Genome Scans for QTL Experiments
| batch_cols | Batch columns by pattern of missing values |
| bayes_int | Calculate Bayes credible intervals |
| calc_sdp | Calculate strain distribution pattern from SNP genotypes |
| cbind.scan1 | Join genome scan results for different phenotypes. |
| cbind.scan1perm | Combine columns from multiple scan1 permutation results |
| chr_lengths | Calculate chromosome lengths |
| decomp_kinship | Calculate eigen decomposition of kinship matrix |
| est_herit | Estimate heritability with a linear mixed model |
| find_peaks | Find peaks in a set of LOD curves |
| fit1 | Fit single-QTL model at a single position |
| genoprob_to_snpprob | Convert genotype probabilities to SNP probabilities |
| get_common_ids | Get common set of IDs from objects |
| index_snps | Create index of equivalent SNPs |
| interp_map | Interpolate between maps |
| invert_sdp | Calculate SNP genotype matrix from strain distribution... |
| lod_int | Calculate LOD support intervals |
| mat2strata | Define strata based on rows of a matrix |
| maxlod | Overall maximum LOD score |
| max_scan1 | Find position with maximum LOD score |
| pick_marker_subset | Identify the largest subset of markers that are some distance... |
| print.summary.scan1perm | Print summary of scan1perm permutations |
| qtl2scan-package | qtl2scan: Genome Scans for QTL Experiments |
| rbind.scan1 | Join genome scan results for different chromosomes. |
| rbind.scan1perm | Combine data from scan1perm objects |
| 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 |
| scan1perm | Permutation test for genome scan with a single-QTL model |
| scan1snps | Single-QTL genome scan at imputed SNPs |
| subset_scan1 | Subset scan1 output |
| summary_scan1perm | Summarize scan1perm results |
| top_snps | Create table of top snp associations |
