Informatics Tools for Cell-Free DNA Study

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Documentation for package ‘cfTools’ version 1.4.0

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

Help Pages

beta_matrix	Beta value matrix
CancerDetector	Cancer Detector
CancerDetector.markers	Cancer-specific marker parameter
CancerDetector.reads	Fragment-level methylation state for cancer detection
cfDeconvolve	cfDNA methylation read deconvolution
cfDeconvolve.markers	Tissue-specific marker parameter
cfDeconvolve.reads	Fragment-level methylation state for tissue deconvolution
cfSort	cfSort: tissue deconvolution
cfSort.reads	Fragment-level methylation state for cfSort tissue deconvolution
cfsort_markers	cfSort markers
CpG_OB_demo	Methylation information for CpG on the original bottom strand (OB)
CpG_OT_demo	Methylation information for CpG on the original top strand (OT)
demo.fragment_level.meth.bed	Fragment-level methylation information
demo.refo_frag.bed	Fragment-level information
demo.refo_meth.bed	Methylation information on fragments
demo.sorted.bed	Paired-end sequencing reads
GenerateFragMeth	Generate fragment-level information about methylation states
GenerateMarkerParam	Generate the methylation pattern of markers
markers.bed	Genomic postions of markers
marker_index	Marker name
MergeCpGs	Generate fragment-level methylation states of CpGs
MergePEReads	Generate fragment-level information for paired-end sequencing reads
sample_type	Sample type