# cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

## Documentation for package ‘cfDNAPro’ version 1.4.0

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

## Help Pages

callMetrics | Calculate the metrics of insert size
callMode | Calculate the mode fragment size of each sample
callPeakDistance | Calculate the inter-peak distance of insert size
callSize | Calculate the insert size metrics (i.e. prop, cdf, 1-cdf) or each group
callValleyDistance | Calculate the inter-valley distance of insert size
examplePath | Get path to cfDNAPro example folder.
plotAllToOne | Plot the raw fragment size metrics (e.g. proportion, cdf and 1-cdf) of all groups with different colors in a single plot
plotMetrics | Plot the fragment size metrics (i.e. proportion, cdf and 1-cdf)
plotMode | Plot mode fragment size
plotModeSummary | Summarize and plot mode fragment size in a stacked bar chart
plotPeakDistance | Plot the inter-peak distance of fragment size distance distribution
plotSingleGroup | Plot the raw fragment size metrics of single group in a single plot, colored by samples.
plotValleyDistance | Plot the inter-valley distance of fragment size distance distribution
readBam | Read bam file into a curated GRanges object
read_bam_insert_metrics | Calculate insert sizes from a curated GRanges object