R/GenVisR.R

In GenVisR: Genomic Visualizations in R

#' GenVisR
#'
#' @name GenVisR
#' @description A visualization library designed to make publications quality figures for genomic datasets.
#' @references \href{https://academic.oup.com/bioinformatics/article/32/19/3012/2196360}{GenVisR: Genomic Visualizations in R}
#' @docType package
#' @seealso \href{https://github.com/griffithlab/GenVisR}{GenVisR github page}
#' @seealso \href{https://www.bioconductor.org/packages/release/bioc/html/GenVisR.html}{GenVisR bioconductor page}
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#' Subset MAF file for PIK3CA gene
#' 
#' A data set originating from the open access TCGA data (6c93f518-1956-4435-9806-37185266d248),
#' the data set is composed of mutations for the PIK3CA gene for breast cancer. This is primarily
#' intended to test the Lolliplot() function.
#' 
#' @docType data
#' @keywords datasets
#' @name PIK3CA
#' @usage data(PIK3CA)
#' @format a data frame with 361 observations and 19 variables
#' @return  Object of class data frame
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#' Truncated BRCA MAF file
#'
#' A data set containing 50 samples corresponding to "Breast invasive carcinoma"
#' originating from the TCGA project in .maf format (version 2.4):
#' https://wiki.nci.nih.gov/display/TCGA/TCGA+MAF+Files#TCGAMAFFiles-BRCA:Breastinvasivecarcinoma, /dccfiles_prod/tcgafiles/distro_ftpusers/anonymous/tumor/brca/gsc/genome.wustl.edu/illuminaga_dnaseq/mutations/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.5.3.0/genome.wustl.edu_BRCA.IlluminaGA_DNASeq.Level_2.5.3.0.somatic.maf
#'
#' @docType data
#' @keywords datasets
#' @name brcaMAF
#' @usage data(brcaMAF)
#' @format a data frame with 2773 observations and 55 variables
#' @return Object of class data drame
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#' Cytogenetic banding dataset
#'
#' A data set containing cytogenetic band information for all chromosomes in the
#' following genomes "hg38", "hg19", "mm10", "mm9", "rn5", obtained from the
#' UCSC sql database at genome-mysql.cse.ucsc.edu.
#'
#' @docType data
#' @keywords datasets
#' @name cytoGeno
#' @usage data(cytoGeno)
#' @format a data frame with 3207 observations and 6 variables
#' @return Object of class data frame
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#' hg19 chromosome boundaries
#'
#' A data set containg chromosome boundaries corresponding to hg19.
#'
#' @docType data
#' @keywords datasets
#' @name hg19chr
#' @usage data(hg19chr)
#' @format a data frame with 24 observations and 3 variables
#' @return Object of class data frame
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#' Truncated CN segments
#'
#' A data set in long format containing Copy Number segments for 4 samples
#' corresponding to "lung cancer" from Govindan et al. Cell. 2012, PMID:22980976
#'
#' @docType data
#' @keywords datasets
#' @name LucCNseg
#' @usage data(LucCNseg)
#' @format a data frame with 3336 observations and 6 variables
#' @return Object of class data frame
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#' Identity snps
#' 
#' A data set containing locations of 24 identity snps originating from:
#' Pengelly et al. Genome Med. 2013, PMID 24070238
#'  
#' @docType data
#' @keywords datasets
#' @name SNPloci
#' @usage data(SNPloci)
#' @format a data frame with 24 observations and 3 variables
#' @return Object of class data frame
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#' Tumor BAM
#' 
#' A data set containing read pileups intersecting 24 identity snp locations
#' from GenVisR::SNPloci. Pileups are from downsampled bams and originate from
#' tumor tissue corresponding to the HCC1395 breast cancer cell line.
#' @docType data
#' @keywords datasets
#' @name HCC1395_T
#' @usage data(HCC1395_T)
#' @format a data frame with 52 observations and 6 variables
#' @return Object of class list
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#' Normal BAM
#' 
#' A data set containing read pileups intersecting 24 identity snp locations
#' from GenVisR::SNPloci. Pileups are from downsampled bams and originate from
#' normal tissue corresponding to the HCC1395 breast cancer cell line.
#' @docType data
#' @keywords datasets
#' @name HCC1395_N
#' @usage data(HCC1395_N)
#' @format a data frame with 59 observations and 6 variables
#' @return Object of class list
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#' Germline Calls
#' 
#' A data set containing downsampled Germline calls originating from the HCC1395
#' breast cancer cell line.
#' @docType data
#' @keywords datasets
#' @name HCC1395_Germline
#' @usage data(HCC1395_Germline)
#' @format a data frame with 9200 observations and 5 variables
#' @return Object of class data frame
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