Quantitative Trait Locus Mapping in Experimental Crosses

add_threshold | Add thresholds to genome scan plot |

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 |

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_het | Calculate heterozygosities |

calc_kinship | Calculate kinship matrix |

calc_raw_founder_maf | Calculate founder minor allele frequencies from raw SNP... |

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_expand | Combine matrices by columns, expanding and aligning rows |

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 |

CCcolors | Collaborative Cross colors |

check_cross2 | Check a cross2 object |

chisq_colpairs | Chi-square test on all pairs of columns |

chr_lengths | Calculate chromosome lengths |

clean | Clean an object |

clean_genoprob | Clean genotype probabilities |

clean_scan1 | Clean scan1 output |

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 |

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 |

decomp_kinship | Calculate eigen decomposition of kinship matrix |

drop_markers | Drop markers from a cross2 object |

drop_nullmarkers | Drop markers with no genotype data |

est_herit | Estimate heritability with a linear mixed model |

est_map | Estimate genetic maps |

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 |

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 |

index_snps | Create index of equivalent SNPs |

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... |

locate_xo | Locate crossovers |

lod_int | Calculate LOD support intervals |

map_to_grid | Subset a map to positions on a grid |

mat2strata | Define strata based on rows of a matrix |

max_compare_geno | Find pair with most similar genotypes |

maxlod | Overall maximum LOD score |

maxmarg | Find genotypes with maximum marginal probabilities |

max_scan1 | Find position with maximum LOD score |

n_missing | Count missing genotypes |

plot_coef | 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... |

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.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 |

qtl2-internal | Internal functions |

qtl2-package | qtl2: Quantitative Trait Locus Mapping in Experimental... |

qtl2version | Installed version of R/qtl2 |

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_csv | Read a csv file |

read_csv_numer | Read a csv file that has numeric columns |

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 |

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 |

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 |

summary_compare_geno | Basic summary of compare_geno object |

summary.cross2 | Summary of cross2 object |

summary_scan1perm | Summarize scan1perm results |

top_snps | Create table of top snp associations |

viterbi | Calculate most probable sequence of genotypes |

write_control_file | Write a control file for QTL data |

xpos_scan1 | Get x-axis position for genomic location |

zip_datafiles | Zip a set of data files |

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