Data import

  • read_cross2 - read data for a cross from a set of files
  • read_csv - read a csv file, using a particular set of options
  • read_csv_numer - like read_csv but assuming the contents are strictly numeric
  • read_pheno - read phenotype data from a CSV file, plus (optionally) phenotype covariate data from a separate CSV file
  • write_control_file - write the control file for a set of QTL data
  • zip_datafiles - zip a set of data files (in the format read by read_cross2)

Data subsetting

  • subset.cross2 - subset a cross2 object by individuals or chromosomes
  • "[".cross2 - shorthand for subset.cross2, with the form mycross[ind, chr]
  • subset.calc_genoprob subset genotype probabilties by indivduals or chromosomes
  • "[".calc_genoprob - shorthand for subset.calc_genoprob, with the form probs[ind, chr]
  • subset.scan1 - subset genome scan results by chromosome or column
  • subset_scan1 - the same as subset.scan1
  • subset.sim_geno - subset genotype imputations by individuals or chromosomes
  • "[".sim_geno - shorthand for subset.sim_geno, with the form simg[ind, chr]
  • subset.viterbi - subset inferred genotypes
  • "[".viterbi - shorthand for subset.viterbi, with the form geno[ind, chr]
  • drop_markers - drop a vector of markers from a "cross2" object
  • drop_nullmarkers - drop markers with no genotypes from a "cross2" object
  • pull_markers - drop all except a vector of markers from "cross2" object

Combining data

  • cbind.calc_genoprob - combine genotype probabilities for multiple chromosomes but on the same set of individuals
  • rbind.calc_genoprob - combine genotype probabilities for different individuals
  • cbind.scan1 - combine genome scan results for multiple phenotypes/analyses
  • rbind.scan1 - combine genome scan results for different chromosomes
  • c.scan1perm - combine genome scan permutation results for multiple replicates
  • cbind.scan1perm - combine genome scan permutation results for multiple phenotypes/analyses
  • rbind.scan1perm - combine genome scan permutation results for multiple chromosomes
  • cbind.sim_geno - combine genotype imputations for multiple chromosomes but on the same set of individuals
  • rbind.sim_geno - combine genotype imputations for different individuals
  • cbind.viterbi - combine inferred genotypes for multiple chromosomes but on the same set of individuals
  • rbind.viterbi - combine inferred genotypes for different individuals

Genotype reconstruction

  • calc_genoprob - calculate conditional genotype probabilities given marker data
  • clean_genoprob - clean up genotype probabilities, setting small values to 0
  • genoprob_to_alleleprob - convert genotype probabilities to allele dosages
  • genoprob_to_snpprob - convert genotype probabilities to SNP probabilities
  • interp_genoprob - linear interpolation of genotype probabilities, for example to get two sets onto the same map for comparison purposes
  • probs_to_grid - subset genotype probabilities to a grid of pseudomarkers
  • pull_genoprobpos - pull out the genotype probabilities for a particular position
  • pull_genoprobint - pull out the genotype probabilities for an interval

Genotype imputation

  • maxmarg - for each individual at each position, find genotype with maximum marginal probability
  • guess_phase - turn imputed genotypes into phased genotypes along chromosomes
  • sim_geno - multiple imputations of underlying genotypes given marker data
  • viterbi - find mostly likely sequence of true genotypes given marker data
  • predict_snpgeno - predict SNP genotypes in a multiparent population from inferred genotypes plus founder strains’ SNP alleles.

Kinship matrix calculations

  • calc_kinship - calculate genetic similarity among individuals
  • decomp_kinship - calculate eigen decomposition of a kinship matrix
  • scale_kinship - scale kinship matrix to be like a correlation matrix

Marker maps

  • est_map - re-estimate the inter-marker distances in a genetic map
  • insert_pseudomarkers - add pseudomarkers into a map of genetic markers
  • calc_grid - Calculate indicators of which pseudomarker positions are along a fixed grid
  • map_to_grid - subset a map object to the locations on some grid
  • interp_map - Use interpolate to convert from one map to another
  • reduce_markers - Reduce marker map to the largest subset that are some distance apart

QTL analysis

  • est_herit - estimate heritability with linear mixed model
  • fit1 - fit a single-QTL model at a single position
  • scan1 - genome scan with a single-QTL model
  • scan1perm - permutation test to establish statistical significance in genome scan
  • scan1coef - calculate QTL effects in scan along one chromosome
  • scan1blup - like scan1coef, but calculating treating QTL effects as random and calculating BLUPs
  • scan1snps - single-QTL scan over SNPs in a multi-parent population

QTL summaries

  • maxlod - calculate genome-wide maximum LOD score in genome scan results
  • max.scan1 - calculate maximum LOD score in genome scan and the position at which it occurred
  • max_scan1 - the same as max.scan1
  • find_peaks - find QTL peaks in genome scan results
  • lod_int - calculate LOD support intervals from genome scan results
  • bayes_int - calculate approximate Bayes intervals for QTL position from genome scan results
  • summary.scan1perm - calculate significance thresholds from genome scan permutation results
  • summary_scan1perm - same as summary.scan1perm
  • top_snps - find the top SNPs from a SNP association scan

Data diagnostics

  • check_cross2 - check for inconsistencies or errors in a "cross2" object
  • calc_entropy - calculate entropy from genotype probabilities, for each individual and position
  • calc_errorlod - calculate genotyping error LOD scores to help identify potential genotyping errors and problem markers or individuals
  • calc_geno_freq - calculate genotype frequencies, by individual or marker, from genotype probabilities
  • chisq_colpairs - Perform chi-square test for independence for all pairs of columns of a matrix
  • convert2cross2 - convert an R/qtl1 "cross" object to the R/qtl2 "cross2" format
  • compare_geno - compare genotypes for all pairs of individuals, to look for possible sample duplicates
  • compare_genoprob - compare two sets of genotype probabilities for one individual on a single chromosome
  • summary.compare_geno - summarize the results of compare_geno
  • summary_compare_geno - same as summary.compare_geno
  • max.compare_geno - from the results of compare_geno, show the pair with most similar genotypes
  • max_compare_geno - same as max.compare_geno
  • count_xo - count the number of crossovers in each individual on each chromosome, from matrices of inferred genotypes
  • locate_xo - locate the positions of crossovers in each individual on each chromosome, from matrices of inferred genotypes.
  • find_ibd_segments - in genotypes of a set of inbred lines, find genomic segments that are identity-by-descent (IBD)
  • compare_maps - compare two marker maps, to identify markers present in one but not the other, or on different chromosomes or in different orders between the maps.
  • find_map_gaps - find large gaps between markers in a genetic map
  • reduce_map_gaps - reduce the lengths of gaps in a genetic map

Data summaries

  • summary.cross2 - summarize a "cross2" object
  • chr_names - names of chromosomes in a "cross2" object
  • marker_names - names of markers in a "cross2" object
  • pheno_names - names of phenotypes in a "cross2" object
  • phenocovar_names - names of “phenotype covariates” (metadata about phenotypes) in a "cross2" object
  • covar_names - names of covariates in a "cross2" object
  • ind_ids - return IDs for all individuals in a "cross2" object
  • ind_ids_geno - return IDs for all individuals in a "cross2" object that have genotype data
  • ind_ids_pheno - return IDs for all individuals in a "cross2" object that have phenotype data
  • ind_ids_gnp - return IDs for all individuals in a "cross2" object that have both genotype and phenotype data
  • ind_ids_covar - return IDs for all individuals in a "cross2" object that have covariate data
  • n_chr - number of chromosomes in a "cross2" object
  • n_ind - number of individuals in a "cross2" object
  • n_ind_geno - number of individuals in a "cross2" object that have genotype data
  • n_ind_pheno - number of individuals in a "cross2" object that have phenotype data
  • n_ind_gnp - number of individuals in a "cross2" object that have both genotype and phenotype data
  • n_ind_covar - number of individuals in a "cross2" object that have covariate data
  • n_mar - number of markers on each chromosome in a "cross2" object
  • tot_mar - total number of markers in a "cross2" object
  • n_pheno - number of phenotypes in a "cross2" object
  • n_covar - number of covariates in a "cross2" object
  • n_phenocovar - number of “phenotype covariates” (metadata on phenotypes) in a "cross2" object
  • chr_lengths - calculate chromosome lengths for a map object
  • find_marker - find marker closest to a particular genomic position
  • find_markerpos - find the position of a marker
  • n_missing - number of missing genotypes, by individual or marker
  • n_typed - number of genotypes, by individual or marker

QTL plots

  • plot.scan1 - plot genome scan results
  • plot_scan1 - same as plot.scan1
  • xpos_scan1 - determine the x-axis location of a particular genomic position in a genome scan plot (for adding annotations)
  • add_threshold - Add horizontal line at a significance threshold to a genome scan plot.
  • plot.scan1coef - plot QTL effects along a chromosome
  • plot_coef - same as plot.scan1coef
  • plot_coefCC - like plot_coef but assuming there are 8 effects and using the standard colors for the Collaborative Cross (CCcolors)
  • plot_snpasso - plot SNP association results
  • plot_genes - plot locations of a set of genes
  • plot_peaks - plot a summary of QTL positions for multiple phenotypes, using the results of find_peaks
  • plot_lodpeaks - scatterplot of LOD scores vs QTL peak locatiosn (possibly with intervals) for multiple traits
  • plot_pxg - plot phenotype versus QTL genotypes

Diagnostic plots

  • plot.calc_genoprob - plot the genotype probabilities for one individual on one chromosome, as a heat map
  • plot_genoprob - the same as plot.calc_genoprob
  • plot_onegeno - plot one individual’s genome-wide genotypes
  • plot_genoprobcomp - plot a comparison of two sets of genotype probabilities for one individual on one chromosome, as a bivariate heat map

SNP/gene databases

  • create_variant_query_func - create a function to connect to a SQLite database of founder variant information and return a data frame with variants for a selected region
  • create_gene_query_func - create a function to connect to a SQLite database of gene annotations and return a data frame with genes in a selected region
  • calc_sdp - convert founder SNP genotypes to a numeric code for the strain distribution pattern
  • invert_sdp - the inverse of calc_sdp
  • index_snps - partition SNPs into groups that are contained within common marker intervals and have the same strain distribution pattern, and create an index to a set of distinct SNPs, one per partition
  • find_index_snp - For a particular SNP, find the corresponding indexed SNP.

Utility functions

  • batch_cols - identify batches of columns of a matrix that have the same pattern of missing values
  • batch_vec - split a vector into batches, for help in balancing parallel code
  • get_common_ids - find IDs that are present in all of the input objects
  • get_x_covar - from a "cross2" object, get the matrix of covariates to be used for the null hypothesis when performing QTL analysis on the X chromosome
  • mat2strata - use the rows of a matrix to define a set of strata for a stratified permutation test
  • replace_ids - Replace the individual IDs in an object
  • replace_ids.calc_genoprob - Replace the individual IDs in a "calc_genoprob" object
  • replace_ids.cross2 - Replace the individual IDs in a "cross2" object
  • replace_ids.sim_geno - Replace the individual IDs in a "sim_geno" object
  • replace_ids.viterbi - Replace the individual IDs in a "viterbi" object
  • align_scan1_map - aligns the markers/pseudomarkers in a "scan1" object (output by scan1()) and a marker map.
  • clean - clean an object
  • clean.scan1 - clean a "scan" object (replacing negative values with NA and removing rows were all values are NA.
  • clean_scan1 - the same as clean.scan1.
  • clean.calc_genoprob - clean a "calc_genoprob" object (setting small values to 0)
  • clean_genoprob - same as clean.calc_genoprob
  • qtl2version - print the installed version of R/qtl2

Boring print functions

  • print.cross2 - print method for a "cross2" object
  • print.summary.cross2 - print method for the output of summary.cross2
  • print.summary.compare_geno - print method for the output of summary.compare_geno
  • print.summary.scan1perm - print method for the output of summary.scan1perm

Other functions

  • calc_het
  • cbind_expand