Man pages for bahlolab/exSTRa
Expanded STR algorithm: detecting expansions in Illumina sequencing data
| add_alpha_ | Add transparency to a color value |
| as.exstra_score | Convert a compatable object to the exstra_score class |
| copy | Copy an object with a data.table. |
| exSTRa | Expanded STR algorithm |
| exstra_known | Known repeat expansion disorder loci. |
| exstra_score_new_ | Create a new exstra_score object |
| exstra_tsum_new_ | Create a new exstra_tsum object. |
| exstra_wgs_pcr_2 | Repeat score data from cohort WGS_PCR_2. |
| filter_low_scores | Filter read scores with lower than expected scores |
| filter_sex | filter rep_score_data by sex |
| ggexstra_ecdf | Create a ggplot2 ecdf plot from an exstra_score object |
| ggplot.exstra_score | Default ggplot method for exstra_score |
| is.exstra_db | check if the object is part of the exstra_db class |
| is.exstra_score | Test if object is an exstra_score object |
| is.exstra_tsum | Check if an object is an instance of the exstra_tsum class. |
| loci | Return the loci of the selected object |
| loci_min_exp | Give the minimum expanded size of the STR |
| loci_normal | Give the reference or normal size of the STR |
| loci_normal_exp | Give the reference or normal size of the STR |
| loci_text_info | Give text info for the locus |
| plot.exstra_score | Plot ECDF curves from an exstra_score object |
| plot.exstra_tsum | Plot exstra_tsum, highlighting significant results |
| plot_multi | Multiple STR score ECDF plots |
| plot_names | Give the plot names for given sample names |
| plot_names-set | Assign the plot names |
| p_values | Return a data.table with p-values of a tsum_exstra object. |
| p_value_sd_ | P-value standard deviation |
| qm_tsum_stat_bare_ | simple tsum statistic by known |
| rbind_score_list | Combine multiple exSTRa data objects. |
| read_exstra_db | Read a file of known STR loci for analysis |
| read_exstra_db_ucsc | Read simple repeats track that's been downloaded from UCSC... |
| read_score | Read repeat score data produced from Bio::STR::exSTRa |
| sub-.exstra_score | Extract loci or samples frome exstra_score object |
| sub-.exstra_tsum | Extract loci or samples from exstra_tsum object |
| suggested_exstra_pipeline | Create a graph of the suggested pipeline |
| tsum_p_value_summary | create summary of significance on a exstra_tsum object |
| tsum_test | Generate T sum statistics and p-values from simulation. |
