Man pages for jjellis/GenomicVis
Genomic Visualisation Routines
| CNVData | An example of a CNV data frame used by 'cnv.heatmap'. |
| CNVExample | An example of a CNV data frame used by 'cnv.plot'. |
| cnv.heatmap | Create a CNV heatmap. |
| cnv.merge | Merge CNVs |
| cnv.plot | Create a copy number and structural variant plot. |
| default.cnv.heatmap.colour.map | CNV heatmap colour scheme. |
| filter.breakdancer | Illustrative funtion to filter Breakdancer calls. |
| gap2cnv | Illustrative function for processing GAP data. |
| genes.in.region | Find gene in a genomic interval |
| GenomicVis | Genomic Visualisation |
| hg19Genes | A 'GRanges' instance that contains hg19 gene locations taken... |
| kataegis | Calculate regions of kataegis from a VCF file. |
| kataegis.colours | Default colours for kataegis plot. |
| KataegisExample | An example of output from the 'kataegis' function. |
| list.vcffiles | List VCF files in a directory. |
| plotKataegis | Plot a kataegis rainfall figure. |
| plot.kataegisList | Create a kataegis "rainfall" plot. |
| prepare.data | Prepare data for plotting. |
| print.kataegisList | Print function for kataegisList |
| read.breakdancer | Illustrative function to read the output of Breakdancer. |
| read.gap | Illustrative function to read GAP output. |
| read.illumina | Illustrative function to an Illumina GenomeStudio file. |
| read.snpeff.vcf | Read a SnpEff annotated VCF file. |
| read.snpeff.vcfs | Illustrative function to read multiple VCFs |
| read.vcf | Read VCF |
| SNPExample | An example of a SNP data frame used by 'cnv.plot'. |
| snv.clustering | Cluster samples based on SNVs. |
| snv.heatmap | Plot a SNV heatmap. |
| summarise.mutations | Summarise the types of mutations in a region of kataegis. |
| SVExample | An example of a structural variant data frame used by... |
| vcf.venn | Create a venn diagram of SNV overlap in a group of VCF files. |
