v_prepareVdata_Circos: Prepare data for module: Circos

In yilixu/vigilante: Visualizing Integrated Genomics in Linked and Nested Translational Elaboration & Knowing Numbers in Genomic Hypothesis Through Statistics

Description

The workflow of vigilante is highly module-based. To ensure a successful and smooth run, vigilante needs to prepare input data before continuing.

Usage

v_prepareVdata_Circos(
  doBAF = FALSE,
  doCNA = FALSE,
  doMB = c(FALSE, "somatic", "germline"),
  doGE = c(FALSE, "log"),
  doFL = FALSE,
  unifyTrackYlim = TRUE
)

Arguments

doBAF	logic, whether to prepare B Allele Frequency (BAF) data, if FALSE, no BAF data will be available for downstream v_Circos function and no BAF track will be shown on Circos plots; if TRUE, please make sure BAF data files are properly named, see Details for more information about file naming.
doCNA	logic, whether to prepare Copy Number Alteration (CNA) data, if FALSE, no CNA data will be available for downstream v_Circos function and no CNA track will be shown on Circos plots; if TRUE, please make sure CNA data files are properly named, see Details for more information about file naming.
doMB	mixed vector, c(FALSE, "somatic", "germline"), whether to prepare Mutation Burden (MB) data, if FALSE, no MB data will be available for downstream v_Circos function and no MB track will be shown on Circos plots; if TRUE, please follow the instruction and run v_llpMultiLoader function first. Also, if TRUE, specify the mutation type, can be either "somatic" or "germline" or both, each type will be shown as a separate track on Circos plots.
doGE	mixed vector, c(FALSE, "log"), whether to prepare Gene Expression (GE) data, if FALSE, no GE data will be available for downstream v_Circos function and no GE track will be shown on Circos plots; if TRUE, please make sure GE data files are properly named, see Details for more information about file naming. Also, if TRUE, specify the value format, can be either "log" or "TPM", choose "TPM" for showing raw TPM value, choose "log" for showing value after log10 conversion (0 will be converted into negative value based on the value range across all samples).
doFL	logic, whether to prepare Fusion Link (FL) data, if FALSE, no FL data will be available for downstream v_Circos function and no FL track will be shown on Circos plots; if TRUE, please make sure FL data files are properly named, see Details for more information about file naming.
unifyTrackYlim	logic, whether to unify each track's y-axis range based on the value range across all samples, default TRUE.

Details

Oftentimes input data files generated by upstream tools came with diverse naming conventions. It might be easy for the user to recognize those files, but not for vigilante if there is no recognizable patterns.

To make input data files clear to vigilante, it would be nice to have them named something like "studyID_sampleID_(other descriptions).file extension". Here "studyID" is the name of the study or project, and it will be used in multiple naming situations (such as on the plot, or in the output file names), so it is recommended to be concise and meaningful.

For module Circos, currently supported input data files are listed below, please contact the author if you want to add more files to the supported list: B Allele Frequency (BAF): *baf.tsv Copy Number Alteration (CNA): *cna.tsv Mutation Burden (MB): see the help file of v_llpMultiLoader function for more information Gene Expression (GE): *cDNA_genes.sf for Salmon Fusion Link (FL): *-fusion-genes.txt for FusionCatcher, *star-fusion*abridged* for STAR-Fusion

Value

list, because R CMD check discourages assignments to the global environment within functions, user needs to run the function with explicitly assigning the return value to a global variable named "prepareVdata_Circos_returnList", which will be a list containing the required variables for downstream analyses.

yilixu/vigilante documentation built on June 4, 2021, 5:07 a.m.