qtl Analysis

as_mapping	Convert to a 'mapping' object.
convert_vcf_to_genfile	Convert VCF data to an 'R/qtl' genotype file.
get_col_indices	Get column indices of object.
get_indices	Get indices of object elements.
get_lod_col_index	Get LOD column index.
get_lod_col_indices	Get LOD column indices.
get_qtl_intervals	Get list of QTL intervals.
get_run_index_list	Get index list of successive runs in a vector.
infer_map_precision	Infer precision of map positions.
isBOOL	Test for a single logical value.
isFALSE	Test for a single 'FALSE' value.
is_mapping	Test if object is a 'mapping'.
is_pseudomarker_id	Test for 'R/qtl' pseudomarker IDs.
is_single_char	Test for a single character.
is_single_nonnegative_number	Test for a single non-negative number.
is_single_nonnegative_whole_number	Test for a single non-negative whole number.
is_single_positive_whole_number	Test for a single positive whole number.
is_single_probability	Test for a single valid probability.
is_single_string	Test for a single character string.
is_valid_id	Test identifier validity.
is_whole_number	Test for whole numbers.
load_seq_dict	Load sequence dictionary from file.
make_geno_matrix	Make genotype matrix from sample and founder genotype data.
make_snp_marker_ids	Make SNP marker IDs for loci.
mapping	Create a 'mapping' object.
mapping_keys	Get keys of a 'mapping' object.
mapping_values	Get values of a 'mapping' object.
parse_snp_marker_ids	Parse SNP marker IDs.
plot_qtl_scanone	Draw a plot of an 'R/qtl' 'scanone' result.
read_samples_from_vcf	Read sample IDs from a VCF file.
read_snps_from_vcf	Read SNP genotypes from VCF files.
remove_na_cols	Remove columns containing only 'NA' values.
validate_mapping	Validate a 'mapping' object.