Man pages for churchill-lab/qtl2api
QTL2 API Library
| calc_correlation | Get the correlation. |
| calc_correlation_plot | Get the correlation data for plotting. |
| calc_founder_coefficients | Get the founder coefficients. |
| calc_lod_peaks_for_annot | Get all the peaks for an id. |
| calc_lod_scores | Perform a LOD scan. |
| calc_lod_scores_by_covar | Perform the LOD scan for each "value" of the interactive... |
| calc_mediation | Perform mediation. |
| calc_rankings | Calculate the rankings for which gene/protein should be... |
| calc_residual_matrix | Calculate the residual matrix. |
| calc_snp_assoc_mapping | Get the SNP association mapping from foundersnps database. |
| get_analysis | Get analysis of the environment for debugging purposes. |
| get_covar_matrix | Create the covar.matrix element. |
| get_data | Get the data from a data from the dataset. |
| get_dataset_by_id | Get the dataset by id (a string). annot_samples can be used... |
| get_dataset_info | Get all "dataset.*" information |
| get_dataset_stats | Get all "dataset.*" statistics. |
| get_expression | Get the expression data. |
| get_lod_peaks | Get the LOD peaks for a dataset. |
| get_lod_peaks_by_covar | Get the LOD peaks for a dataset. |
| get_markers | Get the markers (more for API benefits). Not for qtl2. |
| get_random_id | Get a random identifier from the dataset. |
| get_sample_id_field | Get the sample id field. |
| id_exists | Check if id exists and has data in dataset. |
| invalid | Test if 'val' is invalid. |
| is_phenotype | Check dataset to see if the datatype value is "phenotype" |
| mediation.scan | Mediation Scan. |
| nvl | Check value for validity and return it or a default |
| nvl_int | Convert value to numeric if possible |
| reexports | Objects exported from other packages |
| synchronize_data | Synchronize data and subset accordingly. |
| synchronize_dataset | Get the dataset that is altered to be better use in the... |
| synchronize_samples | Synchronize sample IDs between objects. |
| valid | Test if 'val' is valid. |
| version | Get the version on qtl2api. |
