Package index • hidecan

Internal constructors

new_CAN_data(): CAN_data constructor

new_CUSTOM_data(): CUSTOM_data constructor

new_DE_data(): DE_data constructor

new_GWAS_data(): GWAS_data constructor

new_QTL_data(): QTL_data constructor

validate_CAN_data(): Checks validity of input for CAN_data constructor

validate_CUSTOM_data(): Checks validity of input for CUSTOM_data constructor

validate_DE_data(): Checks validity of input for DE_data constructor

validate_GWAS_data(): Checks validity of input for GWAS_data constructor

validate_QTL_data(): Checks validity of input for QTL_data constructor

Constructors from tibbles

QTL_data(): Creates a QTL_data object

GWAS_data(): Creates a GWAS_data object

DE_data(): Creates a DE_data object

CAN_data(): Creates a CAN_data object

CUSTOM_data(): Creates a CUSTOM_data object

Constructors from packages output

GWAS_data_from_gwaspoly(): Extracts information from GWASpoly output

Computing chromosome length

compute_chrom_length(): Computes chromosomes' length

combine_chrom_length(): Computes chromosomes' length from list

.compute_chrom_length_markers(): Computes chromosomes' length for a tibble of markers

.compute_chrom_length_genes(): Computes chromosomes' length for a tibble of genes

Applying threshold

apply_threshold(): Filters GWAS, DE or QTL mapping results based on a threshold

Plotting functions

hidecan_plot(): Wrapper to create a HIDECAN plot

create_hidecan_plot(): Creates a HIDECAN plot

hidecan_aes(): Default aesthetics for HIDECAN plot

run_hidecan_shiny(): Launches the HIDECAN shiny app

hidecan_plot_from_gwaspoly(): Creates a HIDECAN plot from GWASpoly output

manhattan_plot(): Creates a Manhattan plot

.get_aes_type(): Returns either "aes_type" attribute or object class

.get_plot_aes(): Computes plot aesthetics

.add_data_type(): Add data type to HIDECAN plot

Example datasets

get_example_data(): Example dataset

Utils

.check_cols(): Checks whether some columns are present in a tibble

.check_chroms(): Check chromosomes to plot

.check_chrom_limits(): Check chromosome limits