GRCh2UCSCGRanges        Convert GRCh chromosome format to UCSC style
UCSC2GRChSampleBam      Convert UCSC chromosome format to GRCh style
                        from a list of alignment information
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 sequencing of cell-free DNA
                        (cfDNA)
create_PoN              Create Panel-of-Normal (PoN) object
create_blacklist_gr     Create Blacklist regions GRanges 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
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
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_PoN_files          Read Fragment Profile from a list of rds file
read_bamfile            Read a bam file Read a bam file from give path.
                        Alignment and sequencing read information will
                        be binned into non-overlapping size
segmentByPSCB           Segmentation data with PSCBS
test_isize_KolmogorovSmirnov
                        KolmogorovSmirnov test for insert size
util.bias_correct       Correct GC Bias readcount
zscore_transform        zscore_transform transforms SLRatio profile
                        into z-score
