Man pages for gact/utl
Utility Functions for R/qtl Analysis

as_mappingConvert to a 'mapping' object.
convert_vcf_to_genfileConvert VCF data to an 'R/qtl' genotype file.
get_col_indicesGet column indices of object.
get_indicesGet indices of object elements.
get_lod_col_indexGet LOD column index.
get_lod_col_indicesGet LOD column indices.
get_qtl_intervalsGet list of QTL intervals.
get_run_index_listGet index list of successive runs in a vector.
infer_map_precisionInfer precision of map positions.
isBOOLTest for a single logical value.
isFALSETest for a single 'FALSE' value.
is_mappingTest if object is a 'mapping'.
is_pseudomarker_idTest for 'R/qtl' pseudomarker IDs.
is_single_charTest for a single character.
is_single_nonnegative_numberTest for a single non-negative number.
is_single_nonnegative_whole_numberTest for a single non-negative whole number.
is_single_positive_whole_numberTest for a single positive whole number.
is_single_probabilityTest for a single valid probability.
is_single_stringTest for a single character string.
is_valid_idTest identifier validity.
is_whole_numberTest for whole numbers.
load_seq_dictLoad sequence dictionary from file.
make_geno_matrixMake genotype matrix from sample and founder genotype data.
make_snp_marker_idsMake SNP marker IDs for loci.
mappingCreate a 'mapping' object.
mapping_keysGet keys of a 'mapping' object.
mapping_valuesGet values of a 'mapping' object.
parse_snp_marker_idsParse SNP marker IDs.
plot_qtl_scanoneDraw a plot of an 'R/qtl' 'scanone' result.
read_samples_from_vcfRead sample IDs from a VCF file.
read_snps_from_vcfRead SNP genotypes from VCF files.
remove_na_colsRemove columns containing only 'NA' values.
validate_mappingValidate a 'mapping' object.
gact/utl documentation built on June 1, 2021, 4:24 p.m.