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 |
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