# Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

## Documentation for package ‘cfdnakit’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cfdnakit-package | 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 | Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
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
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 sequencing read information will be binned into non-overlapping size
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 alignment information
util.bias_correct | Correct GC Bias readcount
zscore_transform | zscore_transform transforms SLRatio profile into z-score