Man pages for Pitithat-pu/cfDNAkit
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
| calculate_CES_score | Calculate CES Score from Segmentation |
| call_cnv | Call Copy-number Variation from SLRatio and segmentation |
| cfdnakit-package | Fragmen-length analysis package from high-throughput... |
| create_blacklist_gr | Create Blacklist regions GRanges object |
| create_PoN | Create Panel-of-Normal (PoN) object |
| extract_insert_size | Extract Insert size from SampleBam |
| filter_read_on_blacklist | Filter out reads on blacklist regions |
| fragment_dist | Get insert-size distribution table |
| get_fragment_profile | Getting fragment-length information |
| get_segment_bysolution | Return CNV segmentation result from given all CNV solutions |
| get_solution_table | Get summarised table of cnv solutions |
| get_zscore_profile | Transform SLRatio with PoN Fragment profile |
| GRCh2UCSCGRanges | Convert GRCh chromosome format to UCSC style |
| if_exist_baifile | Check if bai file exist from given bam |
| if_ucsc_chrformat | Check UCSC chromosomes format for input bam file |
| make_density_table | Make Fragment-length density table |
| overlap_bin_with_segment | Overlap and merge bin data frame with segmentation dataframe |
| pipe | Pipe operator |
| plot_cnv_solution | Plot Fragment-length profile with CNV calling result |
| plot_distance_matrix | Plot Distance Matrix from CNVCalling |
| plot_fragment_dist | Plot Fragment-length Distribution |
| plot_sl_ratio | Plot Short/Long-fragment Ratio |
| plot_transformed_sl | Plot z-tranformed Short/Long-fragment Ratio |
| read_bamfile | Read a bam file Read a bam file from give path. Alignment and... |
| read_PoN_files | Read Fragment Profile from a list of rds file |
| segmentByPSCB | Segmentation data with PSCBS |
| test_isize_KolmogorovSmirnov | KolmogorovSmirnov test for insert size |
| UCSC2GRChSampleBam | Convert UCSC chromosome format to GRCh style from a list of... |
| util.bias_correct | Correct GC Bias readcount |
| zscore_transform | zscore_transform transforms SLRatio profile into z-score |
