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

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Documentation for package ‘cfDNAPro’ version 1.11.0

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

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