Man pages for RHReynolds/LDSCforRyten
Run LDSC on Ryten Lab Server
| AddBPWindow | Add window to genes |
| AddGenePosDetails_RemoveXandYandMT | Add gene positional details |
| add_RS_to_GWAS | Find overlapping RS ids in GWAS using genomic co-ordinates. |
| Assimilate_H2_results | Function assembling herirtability results from LD score... |
| Assimilate_H2_results_multipleannot | Assimilate LDSC output from multiple annotations run... |
| Calculate_enrichment_SE_and_logP | Calculate enrichment SE, logP and z-score p-value. |
| Calculate_H2 | Function to run LDSC heritability script for a number of... |
| Calculate_LDscore | Function to calculate LD score for a number of annotations. |
| convert_z_score | Convert z-score to p-value |
| create_annot_file_and_export | Function to create 22 .annot.gz files for each annotation. |
| Create_GWAS_df | Create GWAS dataframe. |
| creating_baseline_df | Function assembling list of SNPs in baseline LD score model |
| df2GRanges | Convert from dataframe to GRanges |
| get_LDSC_fixed_args | Get fixed LDSC arguments. |
| keep_duplicates | Keep duplicates |
| liftover_hg19_to_hg38 | Liftover GWAS from hg19 to hg38 |
| overlap_annot_hits_w_baseline | Map annotation SNPs overlapping the baseline model back to... |
| overlap_annot_list | Find the overlapping SNPs between a list of dataframes... |
| pipe | Pipe operator |
| Plot_H2_coefficient | Plot S-LDSC coefficient p-value per annotation |
| Plot_H2_enrichment_coefficient | Plot S-LDSC H2 enrichment & coefficient per annotation |
| remove_duplicates | Remove duplicates |
