Function reference • RNAsum

All functions

CapStr(): Capitalise input string

REFERENCE_DATASETS: RNAsum Reference Datasets

arriba_pdf_read(): Read Arriba PDF File

arriba_process(): Process Arriba Fusions

arriba_summary_write(): Write Arriba Fusion Summary

arriba_tsv_read(): Read Arriba TSV File

barPlot(): Generate bar-plot for selected genes

cdfPlot(): Generate CDF plot for selected gene

civicDrugTable(): Generate table with drugs targeting selected set of genes

cn_subset(): Copy Number Subset Table

combineDatasets(): Combine sample expression profile with reference datasets

cumsum_ordered(): Calculate cumulative sum

densityPlot(): Generate density and expression distribution plots for selected gene

dragen_fusions_process(): Process DRAGEN Fusions

dragen_fusions_read(): Read DRAGEN Fusions

dragen_mapping_metrics_read(): Read DRAGEN Mapping Metrics

empty_tbl(): Create Empty Tibble Given Column Names

exprGroupStats_groupWise(): Calculate group-wise median, standard deviation, quantiles and cumulative fractions.

exprGroupsStats_geneWise(): Calculate gene-wise median, sd, quantiles and cumulative fractions for expression data

exprTable(): Generate table with coloured cells indicating expression values for selected genes

fusions_annot(): Annotate Fusions with Ensembl Coordinates

fusions_preprocess(): Pre-Process Arriba or DRAGEN Fusions

fusions_summary(): Get Arriba/DRAGEN Fusions Summary

fusions_table(): Fusions Table Display

genes_pcgr_summary(): Get Mutated Genes from PCGR

getColours(): Assign colours to different elements

get_refdata(): Get Reference Data File Paths

get_refgenes(): Get Reference Genes

glanceExprPlot(): Generate boxplot presenting expression profiles for selected set of genes

immune_summary(): Get Immune Gene Summary

known_trans(): Get Known Translocations

known_translocations_cgi_process(): Process CGI Known Translocations

manta_process(): Process Manta Object

mutCNexprPlot(): Generate scatterplot with per-gene expression values (y-axis), CN values (x-axis) and mutation status info (colours), if provided

nearest_position(): Check for nearest value in a vector

pca(): Perform PCA

pcgr_expr(): Get PCGR genes with hits

pcgr_tiers_tsv_read(): Read PCGR Tiers TSV File

perc_rank(): Convert a vector of numbers into corresponding vector of their percentiles

ppl_cnv_som_gene_read(): Read PURPLE CNV Gene File

prepare2write(): Prepare object to write into a file

purple_cnv_summary(): Get PURPLE CNV Summary

rcircos_cyto_info38(): RCircos HG38 CytoBandIdeogram Object

rcircos_plot(): RCircos Plot

read_sample_data(): Read Sample Data

read_wgs_data(): Read WGS Data

rnasum_rmd(): Generate UMCCR RNAsum Report

salmon_counts(): Get Salmon Counts

saveWidgetFix(): Wrapper for saveWidget bug fix

session_info_kable(): Session Information Kable

session_info_tbls(): Session Information Tables

sv_manta_summary(): Get Manta SV Summary

tpm_from_rpkm(): Calculate TPM from RPKM

webplot(): Generate spider web plots to present immunogram genes