Man pages for umccr/gpgr
Genomics Platform Group Reporting

abbreviate_effectAbbreviate SV Effects
af_summaryumccrise AF summary
chord_mantavcf2dfConvert Manta VCF to data.frame
chord_runRun CHORD
cosmic_signatures_2015Get COSMIC 2015 Signatures
count_piecesCount Number of Parts in a String
EFFECT_ABBREVIATIONSAbbreviations for SV effects
get_genome_objGet BSgenome Object
hrdetect_prep_cnvPrepare PURPLE Somatic CNVs for HRDetect
hrdetect_prep_snvindelPrepare VCF with SNVs/INDELs for use with HRDetect
hrdetect_prep_svPrepare VCF with SVs for use with HRDetect
hrdetect_read_purple_cnvRead PURPLE Somatic CNVs for HRDetect
hrdetect_read_snvindel_vcfRead VCF with SNVs/INDELs for use with HRDetect
hrdetect_read_sv_vcfRead VCF with SVs for use with HRDetect
hrdetect_runRun HRDetect via
hrd_results_tabsHRDetect and CHORD Summary Table
is_vcfDoes the input file look like a VCF?
mkdirMake Directory
pkg_existsDoes R Package Exist
plot_bnd_sr_pr_tot_histHistogram for SR, PR and SR + PR for BNDs
plot_bnd_sr_pr_tot_linesLine plot for SR, PR and SR + PR for BNDs
process_svProcess Structural Variants
purple_cnv_germ_processProcess PURPLE CNV germline File for UMCCRISE
purple_cnv_germ_readRead PURPLE CNV Germline File
purple_cnv_som_gene_processProcess PURPLE CNV Gene File for UMCCRISE
purple_cnv_som_gene_readRead PURPLE CNV Gene File
purple_cnv_som_processProcess PURPLE CNV Somatic File for UMCCRISE
purple_cnv_som_readRead PURPLE CNV Somatic File
purple_kataegisGet PURPLE Kataegis Regions
purple_purity_readRead PURPLE Purity file
purple_qc_readRead PURPLE QC file
purple_snv_vcf_readRead PURPLE Somatic SNV VCF
purple_version_readRead PURPLE version file
sig_contributionCalculate COSMIC Signature Contribution
sig_contribution_tableCreate COSMIC Signature Table
sig_count_dbsCount DBS Contexts
sig_count_indelCount INDEL Contexts
sig_count_snvCount SNV Contexts
sig_plot_dbsPlot DBS Mutation Characteristics
sig_plot_indelPlot INDEL Mutation Characteristics
sig_plot_snvPlot SNV Mutation Characteristics
sig_workflow_runRun MutationalPatterns Workflow
split_double_colSplit Two-Field Column
tidyevalTidy eval helpers
tsv_is_emptyDoes the TSV file contain any non-header rows?
umccrise_read_sv_tsvRead SV TSV
vcf_is_emptyDoes the VCF file contain any variants?
write_jsongzWrite gzipped JSON
write_tsvgzWrite a data frame to a tab delimited gzipped file
write_tsvjsongzWrite a data frame to gzipped TSV and JSON files
umccr/gpgr documentation built on Nov. 25, 2021, 1:15 p.m.