# Informatics Tools for Cell-Free DNA Study

## 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