Man pages for steveped/ngsReports
Load FastqQC reports and other NGS related files
| dot-addPercent | Add a percentage sign |
| dot-emptyPlot | Create an empty plot with supplied text |
| dot-FastpFile-class | The .FastpFile Object Class |
| dot-FastqcFile-class | The .FastqcFile Object Class |
| dot-getToolName | Identify tool name |
| dot-hidePWFRects | Hide PWF tooltips from line plots |
| dot-makeDendro | Make the dendrogram for heatmap-style plots |
| dot-makeLabels | Perform the checks and return the labels |
| dot-makePwfGradient | Construct a gradient using PwfCols |
| dot-makeSidebar | Shortcut for making the status sidebar |
| dot-parseAdapterRemovalLogs | Parse data from Adapter Removal log files |
| dot-parseBowtieLogs | Parse data from Bowtie log files |
| dot-parseBuscoLogs | Parse data from BUSCO log files |
| dot-parseCutadaptLogs | Parse data from cutadapt log files |
| dot-parseDuplicationMetricsLogs | Parse data from Picard duplicationMetrics log files |
| dot-parseFeatureCountsLogs | Parse data from featureCounts summary files |
| dot-parseFlagstatLogs | Parse data from samtools flagstat files |
| dot-parseHisat2Logs | Parse data from HISAT2 log files |
| dot-parseMacs2CallpeakLogs | Parse data from macs2 callpeak log files |
| dot-parseQuastLogs | Parse data from BUSCO log files |
| dot-parseRnaseqcMetricsLogs | Parse data from rnaseqc metrics files |
| dot-parseSalmonLibFormatCountsLogs | Parse data from salmon lib_format_counts.json files |
| dot-parseSalmonMetaInfoLogs | Parse data from salmon meta_info.json files |
| dot-parseStarLogs | Parse data from STAR log files |
| dot-parseTrimmomaticLogs | Parse data from trimmomatic log files |
| dot-parseUmitoolsDedupLogs | Parse data from umi_tools dedup files |
| dot-prepHeatmap | Prepare the final heatmap for plotting |
| dot-renderDendro | Set up dendrograms for interactive plots |
| dot-splitByTab | Split elements of a vector into a data.frame |
| dot-updateThemeFromDots | Add custom theme elements from dotArgs |
| estGcDistn | Estimate a GC Content Distribution From Sequences |
| extract-methods | Extract Elements |
| FastpData | The FastpData Object Class |
| FastpDataList | The FastpDataList Object Class |
| FastqcData | The FastqcData Object Class |
| FastqcDataList | The FastqcDataList Object Class |
| fqcVersion | Get the FASTQC version |
| fqName-methods | Return the Underlying Fastq File Names from Fastqc/Fastp... |
| gcAvail | List Genomes or Transcriptomes with Theoretical GC Content |
| gcTheoretical | Theoretical GC content |
| getColours-methods | Work with objects of class PwfCols |
| getGC | Get Theoretical GC content |
| getModule | Retrieve a given module from a Fastqc* Object |
| getSummary | Get the summary information from Fastqc Files |
| importNgsLogs | Import Various NGS-related log files |
| importSJ | Import STAR Splice Junctions |
| isCompressed | Check to see if a file is compressed |
| maxAdapterContent | Get the maximum Adapter Content |
| mData | Extract Metadata for TheoreticalGC objects |
| overRep2Fasta-methods | Write fasta of Over-Represented sequences. |
| path | Return the File Paths from an object |
| plotAdapterContent-methods | Draw an Adapter Content Plot |
| plotAlignmentSummary | Plot a summary of alignments |
| plotAssemblyStats | Plot a summary of assembly logs |
| plotBaseQuals-methods | Plot the Base Qualities for each file |
| plotDupLevels-methods | Plot the combined Sequence_Duplication_Levels information |
| plotFastqcPCA-methods | Draw a PCA plot for Fast QC modules |
| plotGcContent-methods | Plot the Per Sequence GC Content |
| plotInsertSize-methods | Plot Insert Size Distributions |
| plotKmers-methods | Plot Overrepresented Kmers |
| plotNContent-methods | Draw an N Content Plot |
| plotOverrep-methods | Plot a summary of Over-represented Sequences |
| plotReadTotals-methods | Draw a barplot of read totals |
| plotSeqContent-methods | Plot the per base content as a heatmap |
| plotSeqLengthDistn-methods | Plot the Sequence Length Distribution |
| plotSeqQuals-methods | Plot the Per Sequence Quality Scores |
| plotSummary-methods | Plot the PASS/WARN/FAIL information |
| pwf | Colours for PASS/WARN/FAIL |
| PwfCols-class | The PwfCols class and associated methods |
| readTotals | Get the read totals |
| summariseOverrep-methods | Summarise Overrepresented Sequences |
| TheoreticalGC-class | The TheoreticalGC Object Class |
| writeHtmlReport | Write an HTML Summary Report |
