Man pages for bahlolab/varpr
Prioritises variants from the merged_collab file
| are_exosplice_vars | Which variants are within exonic, splicing or exonic/splicing... |
| are_in_lr | Is the specific variant/row located within the provided... |
| are_rare_vars | Which variants are rare in the genomic databases? |
| are_synsnv_vars | Which variants are synonymous SNVs? |
| clean_genes | Cleans a vector of genes |
| format_comma | Format numbers with commas for pretty printing |
| format_dec | Format floating point numbers with two decimals for pretty... |
| gt_tab_per_fam | Genotype table per family. |
| gt_tab_per_sample | Genotype table per sample. |
| is_gt_col | Which columns are genotype columns? |
| is_gt_col_for_fam | Which columns are genotype columns for the specified family? |
| is_rare_in | Check if this atomic vector is NA or less than a specified... |
| maf_tab | Returns a summary of a MAF variable (i.e. 1KG or ESP6500) |
| read_var_file | Read in a variant file. |
| read_var_obj | Read in a variant file stored as an rds object. |
| shorten_change | Shorten change column from variant file |
| shorten_pph2 | Shorten PPH2 column from variant file |
| shorten_refalt | Shorten REF/ALT column from variant file |
| shorten_region | Shorten region column from variant file |
| shorten_sift | Shorten SIFT column from variant file |
| tidy_vars | Tidy up the vars data frame |
| var_all_ok | Are the variable classes and names for the vars as expected? |
| var_cl_main_ok | Are the main var columns of the expected class? |
| var_cl_sample_ok | Are the sample var columns of the expected class? |
| var_names_ok | Are the names of the main var columns as expected? |
| varpr | varpr: A package for variant prioritisation. |
| vartype_count | Counts the number of SNVs and INDELs. |
| vartype_count_per_chr | Counts the number of SNVs and INDELs within each chromosome |
