Man pages for hw538/cfDNAPro
cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA
| bam_to_galp2 | Function to read bam file |
| callCNV | Call Copy Number Variation Using QDNAseq Utilities |
| callLength | Call Fragment Length |
| callMetrics | Calculate the metrics of insert size |
| callMode | Calculate the mode fragment size of each sample |
| callMotif | Call Motif |
| callPeakDistance | Calculate the inter-peak distance of insert size |
| callSize | Calculate the insert size metrics (i.e. prop, cdf, 1-cdf) or... |
| callTrinucleotide | Call trinucleotides and summarise the cfDNA information for... |
| callValleyDistance | Calculate the inter-valley distance of insert size |
| downsampleBam | Randomly Downsample BAM File to a Target Depth |
| examplePath | Get path to cfDNAPro example folder. |
| pileupMismatches | Pileup Mismatches from BAM Files |
| plotAllToOne | Plot the raw fragment size metrics (e.g. proportion, cdf and... |
| plotCNV | plot copy number profile |
| plotLength | Plot fragment length profile |
| plotMetrics | Plot the fragment size metrics (i.e. proportion, cdf and... |
| plotMode | Plot mode fragment size |
| plotModeSummary | Summarize and plot mode fragment size in a stacked bar chart |
| plotMotif | Plot Motif Count or Fraction as Bar Plot |
| plotPeakDistance | Plot the inter-peak distance of fragment size distance... |
| plotSingleGroup | Plot the raw fragment size metrics of single group in a... |
| plotTrinucleotide | Plot Trinucleotide SBS Data |
| plotValleyDistance | Plot the inter-valley distance of fragment size distance... |
| processMotif | Helper function to process the motif data |
| readBam | Read bam file into a curated GRanges object |
| read_bam_insert_metrics | Calculate insert sizes from a curated GRanges object |
| readGALP | Read bam file into GAlignmentPairs object |
| summarizeBam | Summarise descriptive Bam stats |
| writeMutTable | Function that generates a Mutation Table with summarised... |
