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

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Documentation for package ‘cfdnakit’ version 1.6.0

• 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