Package 'BubbleTree'

Title: BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
Description: CNV analysis in groups of tumor samples.
Authors: Wei Zhu <[email protected]>, Michael Kuziora <[email protected]>, Todd Creasy <[email protected]>, Brandon Higgs <[email protected]>
Maintainer: Todd Creasy <[email protected]>, Wei Zhu <[email protected]>
License: LGPL (>= 3)
Version: 2.35.0
Built: 2024-07-15 05:19:25 UTC
Source: https://github.com/bioc/BubbleTree

Help Index

all.somatic.lst

Description

A dataset containing pre-calculated BAF scores for annotated SNVs.

Format

S4 object with seqnames, genomic ranges, strand, BAF score

Source

internal

allCall.lst

Description

A dataset containing precalculated data from CNV segment analysis.

Format

S4 object with rbd, rbd.adj, results

Source

internal

allCNV.lst

Description

A dataset containing pre-calculated segment calls.

Format

S4 object with seqnames, genomic ranges, num.mark, score

Source

internal

allHetero.lst

Description

S4 GRanges dataset containing pre-calculated heterozygosity data.

Format

S4

Source

internal

allRBD.lst

Description

A dataset containing precalculated data from CNV segment analysis.

Format

S4 object with rbd, rbd.adj

Source

internal

annoByGenesAndCyto

Description

get annotation for genes and cytobands

Usage

annoByGenesAndCyto(.Object, chr, beg, end, critical.genes, gene.uni.clean.gr,
  cyto.gr)

## S4 method for signature 'Annotate'
annoByGenesAndCyto(.Object, chr, beg, end, critical.genes,
  gene.uni.clean.gr, cyto.gr)

Arguments

.Object

the objet
chr

the chromosome
beg

genomic start coord
end

genomic end coord
critical.genes

set of critical genes
gene.uni.clean.gr

gr object of genes
cyto.gr

gr object of cyto positions

Value

list of annotation for genes and cytobands

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree"))
load(system.file("data", "vol.genes.rda", package="BubbleTree"))
load(system.file("data", "gene.uni.clean.gr.rda", package="BubbleTree"))
load(system.file("data", "cyto.gr.rda", package="BubbleTree"))

comm <- btcompare(vol.genes, cancer.genes.minus2)
btreeplotter <- new("BTreePlotter", branch.col="gray50")
annotator <-new("Annotate")
nn <- "sam2"
cc <- allCall.lst[[nn]]
z <- drawBTree(btreeplotter, cc@rbd.adj) + 
    ggplot2::labs(title=sprintf("%s (%s)", nn, info(cc)))
out <- cc@result$dist  %>% 
    filter(seg.size >= 0.1 ) %>% 
    arrange(gtools::mixedorder(as.character(seqnames)), start)

ann <- annoByGenesAndCyto(annotator,
                   as.character(out$seqnames),
                   as.numeric(out$start),
                   as.numeric(out$end),
                   comm$comm,
                   gene.uni.clean.gr=gene.uni.clean.gr,
                   cyto.gr=cyto.gr)

Annotate

Description

Annotate

Examples

annotate <- new("Annotate")

bafTrack

Description

get the BAF track

Usage

bafTrack(.Object, result.dat, gr2, somatic.gr = NULL, min.prev = 0.15,
  cex = 1.2)

## S4 method for signature 'TrackPlotter'
bafTrack(.Object, result.dat, gr2, somatic.gr = NULL,
  min.prev = 0.15, cex = 1.2)

Arguments

.Object

the object
result.dat

the result dataframe
gr2

the gr2 object
somatic.gr

somatic gr object annotation
min.prev

previous min
cex

the cex

Value

the highlighted BAF track

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "centromere.dat.rda", package="BubbleTree"))
load(system.file("data", "all.somatic.lst.RData", package="BubbleTree"))
load(system.file("data", "hg19.seqinfo.rda", package="BubbleTree"))

trackplotter <- new("TrackPlotter")
gr2 = centromere.dat
nn <- "sam2"
p2 <- bafTrack(trackplotter,
               result.dat=allCall.lst[[nn]]@result,
               gr2=gr2,
               somatic.gr=all.somatic.lst[[nn]])

btcompare

Description

btcompare

Usage

btcompare(set1, set2)

Arguments

set1

first set
set2

second set to compare

Value

combined, unique list of genes

Examples

load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree"))
load(system.file("data", "vol.genes.rda", package="BubbleTree"))

# 77 common cancer genes
comm <- btcompare(vol.genes, cancer.genes.minus2)

btpredict

Description

btpredict

Usage

btpredict(.Object)

## S4 method for signature 'BTreePredictor'
btpredict(.Object)

Arguments

.Object

the object

Value

.Object populated with the predictions

Examples

load(system.file("data", "allRBD.lst.RData", package="BubbleTree"))

btreepredictor <- new("BTreePredictor")
btreepredictor@config$cutree.h <- 0.15
high.ploidy <- rep(TRUE, length(allRBD.lst))
high.purity <- rep(TRUE, length(allRBD.lst))

high.ploidy[c("sam6",
              "ovary.wgs",
              "ovary.wes",
              "TCGA-06-0145-01A-01W-0224-08",
              "TCGA-13-1500-01A-01D-0472-01",
              "TCGA-AO-A0JJ-01A-11W-A071-09")] <- FALSE

high.purity[c("sam6", "ovary.wgs", "ovary.wes")] <- FALSE

rbd <- allRBD.lst[["sam6"]]
btreepredictor@config$high.ploidy <- high.ploidy["sam6"]
btreepredictor@config$high.purity <- high.purity["sam6"]
btreepredictor <- loadRBD(btreepredictor, rbd)
btreepredictor@config$min.segSize <- ifelse(max(btreepredictor@rbd$seg.size, 
                                                na.rm=TRUE) < 0.4, 0.1, 0.4)
btreepredictor <- btpredict(btreepredictor)
cat(info(btreepredictor), "\n")

BTreePlotter

Description

BTreePlotter

Examples

btreeplotter <- new("BTreePlotter")

BTreePredictor

Description

BTreePredictor

Examples

btreepredictor <- new("BTreePredictor")

cancer.genes.minus2.rda

Description

A dataset containing a list of known cancer genes.

Format

list

Source

internal

centromere.dat

Description

A dataset containing an annotated list of centromere locations.

Format

list

Source

internal

cnv.gr

Description

S4 GRanges object containing data on chromosomal locations with seqnames, genomic range, strand, name

Format

S4

Source

internal

cyto.gr

Description

S4 GRanges object containing data on chromosomal locations with seqnames, genomic range, strand, name, gieStain.

Format

S4

Source

internal

drawBTree

Description

draw the BTree track

Usage

drawBTree(.Object, rbd, size = 1)

## S4 method for signature 'BTreePlotter'
drawBTree(.Object, rbd, size = 1)

Arguments

.Object

the object
rbd

the rbd object
size

the size

Value

draw the BTree track

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree"))
load(system.file("data", "vol.genes.rda", package="BubbleTree"))
load(system.file("data", "gene.uni.clean.gr.rda", package="BubbleTree"))
load(system.file("data", "cyto.gr.rda", package="BubbleTree"))

# 77 common cancer genes
comm <- btcompare(vol.genes, cancer.genes.minus2)

btreeplotter <- new("BTreePlotter", branch.col="gray50")
annotator <-new("Annotate")
cc <- allCall.lst[["sam2"]]
z <- drawBTree(btreeplotter, cc@rbd.adj) + 
    ggplot2::labs(title=sprintf("%s (%s)", "sam2", info(cc)))

drawBubbles

Description

draw the Bubbles

Usage

drawBubbles(.Object, rbd, col = NULL)

## S4 method for signature 'BTreePlotter'
drawBubbles(.Object, rbd, col = "gray80")

Arguments

.Object

the object
rbd

the rbd object
col

the col value

Value

draw the bubbles on the track

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))

btreeplotter <- new("BTreePlotter", max.ploidy=5, max.size=10)
nn <- "sam2"
rbd1 <- allCall.lst[[nn]]@rbd
rbd2 <- allCall.lst[[nn]]@rbd.adj
arrows <- trackBTree(btreeplotter, rbd1, rbd2, min.srcSize=0.01, 
                     min.trtSize=0.01)
btree <- drawBTree(btreeplotter, rbd1) + 
    drawBubbles(btreeplotter, rbd2, "gray80") + arrows

drawFeatures

Description

draw the features

Usage

drawFeatures(.Object, rbd, col = NULL)

## S4 method for signature 'BTreePlotter'
drawFeatures(.Object, rbd, col = "black")

Arguments

.Object

the object
rbd

the rbd object
col

the col value

Value

draw the annotation on the track

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree"))
load(system.file("data", "vol.genes.rda", package="BubbleTree"))
load(system.file("data", "gene.uni.clean.gr.rda", package="BubbleTree"))
load(system.file("data", "cyto.gr.rda", package="BubbleTree"))

# 77 common cancer genes merged from 2 sets
comm <- btcompare(vol.genes, cancer.genes.minus2)

btreeplotter <- new("BTreePlotter", branch.col="gray50")
annotator <- new("Annotate")

nn <- "sam12"
cc <- allCall.lst[[nn]]
z <- drawBTree(btreeplotter, cc@rbd.adj) + 
    ggplot2::labs(title=sprintf("%s (%s)", nn, info(cc)))
out <- cc@result$dist  %>% filter(seg.size >= 0.1 ) %>% 
    arrange(gtools::mixedorder(as.character(seqnames)), start)

ann <- with(out, {
    annoByGenesAndCyto(annotator,
                       as.character(out$seqnames),
                       as.numeric(out$start),
                       as.numeric(out$end),
                       comm$comm,
                       gene.uni.clean.gr=gene.uni.clean.gr,
                       cyto.gr=cyto.gr)
})

out$cyto <- ann$cyto
out$genes <- ann$ann
v <- z + drawFeatures(btreeplotter, out)
print(v)

gene.uni.clean.gr

Description

S4 GRanges object containing human gene annotation with seqnames, genomic coordinates, stand, gene.sybmol.

Format

S4

Source

internal

getTracks

Description

get all tracks

Usage

getTracks(p1, p2, title = "")

Arguments

p1

set 1
p2

set 2
title

the title

Value

all of the requested tracks

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "centromere.dat.rda", package="BubbleTree"))
load(system.file("data", "all.somatic.lst.RData", package="BubbleTree"))
load(system.file("data", "hg19.seqinfo.rda", package="BubbleTree"))

trackplotter <- new("TrackPlotter")
gr2 = centromere.dat
nn <- "sam2"
ymax <- ifelse(nn %in% c("lung.wgs", "lung.wes"), 9, 4.3)
p1 <- xyTrack(trackplotter,
              result.dat=allCall.lst[[nn]]@result,
              gr2=gr2,
              ymax=ymax) + ggplot2::labs(title=nn)

p2 <- bafTrack(trackplotter,
               result.dat=allCall.lst[[nn]]@result,
               gr2=gr2,
               somatic.gr=all.somatic.lst[[nn]])

t1 <- getTracks(p1, p2)

heteroLociTrack

Description

get the heteroLoci track

Usage

heteroLociTrack(.Object, result.dat, gr2, hetero.gr = NULL, min.prev = 0.15,
  ymax = 4.3, cex = 0.5)

## S4 method for signature 'TrackPlotter'
heteroLociTrack(.Object, result.dat, gr2,
  hetero.gr = NULL, min.prev = 0.15, ymax = 4.3, cex = 0.5)

Arguments

.Object

the object
result.dat

the results
gr2

the gr2 object
hetero.gr

hetero annotation
min.prev

previous min
ymax

max y
cex

the cex

Value

the highlightted heterozygosity track

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "centromere.dat.rda", package="BubbleTree"))
load(system.file("data", "allHetero.lst.RData", package="BubbleTree"))
load(system.file("data", "hg19.seqinfo.rda", package="BubbleTree"))


trackplotter <- new("TrackPlotter")
gr2 = centromere.dat
nn <- "sam2"
z1 <- heteroLociTrack(trackplotter, allCall.lst[[nn]]@result, 
                      gr2, allHetero.lst[[nn]])

hg19.seqinfo.Rd

Description

Seqinfo object containing names and lengths of each chromosome of the human genome.

Format

Seqinfo

Source

internal

info

Description

info

Usage

info(.Object)

## S4 method for signature 'BTreePredictor'
info(.Object)

Arguments

.Object

the object

Value

print out info of prediction data

Examples

load(system.file("data", "allRBD.lst.RData", package="BubbleTree"))

btreepredictor <- new("BTreePredictor")
btreepredictor@config$cutree.h <- 0.15


high.ploidy <- rep(TRUE, length(allRBD.lst))
high.purity <- rep(TRUE, length(allRBD.lst))

high.ploidy[c("sam6",
              "ovary.wgs",
              "ovary.wes",
              "TCGA-06-0145-01A-01W-0224-08",
              "TCGA-13-1500-01A-01D-0472-01",
              "TCGA-AO-A0JJ-01A-11W-A071-09")] <- FALSE

high.purity[c("sam6", "ovary.wgs", "ovary.wes")] <- FALSE

nn <- "sam6"

rbd <- allRBD.lst[[nn]]
btreepredictor@config$high.ploidy <- high.ploidy[nn]
btreepredictor@config$high.purity <- high.purity[nn]
btreepredictor <- loadRBD(btreepredictor, rbd)
btreepredictor@config$min.segSize <- ifelse(max(btreepredictor@rbd$seg.size, 
                                                na.rm=TRUE) < 0.4, 0.1, 0.4)
btreepredictor <- btpredict(btreepredictor)
cat(info(btreepredictor), "\n")

loadRBD

Description

load the RBD data

Usage

loadRBD(.Object, rbd, total.mark = NA)

## S4 method for signature 'BTreePredictor'
loadRBD(.Object, rbd, total.mark = NA)

Arguments

.Object

the object
rbd

rbd object
total.mark

total mark

Value

.Object populated with the RBD list with updated segment size

Examples

load(system.file("data", "allRBD.lst.RData", package="BubbleTree"))

btreepredictor <- new("BTreePredictor")
btreepredictor@config$cutree.h <- 0.15

high.ploidy <- rep(TRUE, length(allRBD.lst))
high.purity <- rep(TRUE, length(allRBD.lst))

high.ploidy[c("sam6",
              "ovary.wgs",
              "ovary.wes",
              "TCGA-06-0145-01A-01W-0224-08",
              "TCGA-13-1500-01A-01D-0472-01",
              "TCGA-AO-A0JJ-01A-11W-A071-09")] <- FALSE

high.purity[c("sam6", "ovary.wgs", "ovary.wes")] <- FALSE

nn <- "sam6"

rbd <- allRBD.lst[[nn]]
btreepredictor@config$high.ploidy <- high.ploidy[nn]
btreepredictor@config$high.purity <- high.purity[nn]
btreepredictor <- loadRBD(btreepredictor, rbd)

makeRBD

Description

make the RBD object

Usage

makeRBD(.Object, ...)

## S4 method for signature 'RBD'
makeRBD(.Object, snp.gr, cnv.gr, unimodal.kurtosis = -0.1)

Arguments

.Object

the object
...

other input (not needed)
snp.gr

SNP GenomicRanges object
cnv.gr

CNV GenomicRanges object
unimodal.kurtosis

kurtosis

Value

RBD object

Examples

# load sample files
load(system.file("data", "cnv.gr.rda", package="BubbleTree"))
load(system.file("data", "snp.gr.rda", package="BubbleTree"))

# load annotations
load(system.file("data", "centromere.dat.rda", package="BubbleTree"))
load(system.file("data", "cyto.gr.rda", package="BubbleTree"))
load(system.file("data", "cancer.genes.minus2.rda", package="BubbleTree"))
load(system.file("data", "vol.genes.rda", package="BubbleTree"))
load(system.file("data", "gene.uni.clean.gr.rda", package="BubbleTree"))


# initialize RBD object
r <- new("RBD", unimodal.kurtosis=-0.1)

# create new RBD object with GenomicRanges objects for SNPs and CNVs
rbd <- makeRBD(r, snp.gr, cnv.gr)
head(rbd)

# create a new prediction
btreepredictor <- new("BTreePredictor", rbd=rbd, max.ploidy=6, prev.grid=seq(0.2,1, by=0.01))
pred <- btpredict(btreepredictor)

# create rbd plot
btreeplotter <- new("BTreePlotter", max.ploidy=5, max.size=10)
btree <- drawBTree(btreeplotter, pred@rbd)
print(btree)

# create rbd.adj plot
btreeplotter <- new("BTreePlotter", branch.col="gray50")
btree <- drawBTree(btreeplotter, pred@rbd.adj)
print(btree)

# create a combined plot with rbd and rbd.adj that shows the arrows indicating change
# THIS IS VERY MESSY WITH CURRENT DATA from Dong
btreeplotter <- new("BTreePlotter", max.ploidy=5, max.size=10)
arrows <- trackBTree(btreeplotter,
                     pred@rbd,
                     pred@rbd.adj,
                     min.srcSize=0.01, 
                     min.trtSize=0.01)

btree <- drawBTree(btreeplotter, pred@rbd) + arrows 
print(btree)


# create a plot with overlays of significant genes
btreeplotter <- new("BTreePlotter", branch.col="gray50")
annotator <- new("Annotate")

comm <- btcompare(vol.genes, cancer.genes.minus2)

sample.name <- "22_cnv_snv"

btree <- drawBTree(btreeplotter, pred@rbd.adj) + 
    ggplot2::labs(title=sprintf("%s (%s)", sample.name, info(pred)))

out <- pred@result$dist  %>% 
    filter(seg.size >= 0.1 ) %>% 
    arrange(gtools::mixedorder(as.character(seqnames)), start)

ann <- with(out, {
    annoByGenesAndCyto(annotator,
                       as.character(out$seqnames),
                       as.numeric(out$start),
                       as.numeric(out$end),
                       comm$comm,
                       gene.uni.clean.gr=gene.uni.clean.gr,
                       cyto.gr=cyto.gr)
})

out$cyto <- ann$cyto
out$genes <- ann$ann

btree <- btree + drawFeatures(btreeplotter, out)
print(btree)


# print out purity and ploidy values
info <- info(pred)
cat("\nPurity/Ploidy: ", info, "\n")

mergeSnpCnv

Description

merge snp and cnv data

Usage

mergeSnpCnv(.Object, snp.gr, cnv.gr)

## S4 method for signature 'RBD'
mergeSnpCnv(.Object, snp.gr, cnv.gr)

Arguments

.Object

the object
snp.gr

SNP GenomicRanges object
cnv.gr

CNV GenomicRanges object

Value

combined, unique list of genes

RBD

Description

RBD

Examples

rbd <- new("RBD")

RscoreTrack

Description

get the RScore track

Usage

RscoreTrack(.Object, result.dat, gr2, cnv.gr = NULL, min.prev = 0.15,
  ymax = 3, cex = 1.5)

## S4 method for signature 'TrackPlotter'
RscoreTrack(.Object, result.dat, gr2, cnv.gr = NULL,
  min.prev = 0.15, ymax = 3, cex = 1.5)

Arguments

.Object

the object
result.dat

the results
gr2

the gr2 object
cnv.gr

cnv annotation
min.prev

previous min
ymax

max y
cex

the cex

Value

the highlighted RScore track

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "centromere.dat.rda", package="BubbleTree"))
load(system.file("data", "allCNV.lst.RData", package="BubbleTree"))
load(system.file("data", "hg19.seqinfo.rda", package="BubbleTree"))

gr2 = centromere.dat
trackplotter <- new("TrackPlotter")
nn <- "sam2"
z <- RscoreTrack(trackplotter, allCall.lst[[nn]]@result, gr2, allCNV.lst[[nn]])

saveXLS

Description

saveXLS

Usage

saveXLS(dat.lst, xls.fn, row.names = FALSE, ...)

Arguments

dat.lst

dataframe
xls.fn

filename
row.names

row names
...

misc

Value

new Excel file

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))

all.summary <- plyr::ldply(allCall.lst, function(.Object) {
    purity <- .Object@result$prev[1]
    adj <- .Object@result$ploidy.adj["adj"]
    # when purity is low the calculation result is not reliable
    ploidy <- (2*adj -2)/purity + 2  
    
    with(.Object@result,
         return(c(Purity=round(purity,3),
                  Prevalences=paste(round(prev,3), collapse=", "),
                  "Tumor ploidy"=round(ploidy,1))))
}) %>% plyr::rename(c(".id"="Sample"))

xls.filename <- paste("all_summary", "xlsx", sep=".")
saveXLS(list(Summary=all.summary), xls.filename)

snp.gr

Description

S4 GRanges object containing data on chromosomal locations with seqnames, genomic position, strand, name

Format

S4

Source

internal

trackBTree

Description

get the geom_segment location of the BTree track

Usage

trackBTree(.Object, rbd1, rbd2, is.matched = FALSE, min.srcSize = 0.5,
  min.trtSize = 0.1, min.overlap = 1e+05)

## S4 method for signature 'BTreePlotter'
trackBTree(.Object, rbd1, rbd2, is.matched = FALSE,
  min.srcSize = 0.5, min.trtSize = 0.1, min.overlap = 1e+05)

Arguments

.Object

the object
rbd1

rbd one
rbd2

rbd two
is.matched

is it matched
min.srcSize

min src size
min.trtSize

min trt size
min.overlap

min overlap

Value

geom_segment location of BTree track

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))

btreeplotter <- new("BTreePlotter", max.ploidy=5, max.size=10)
nn <- "sam2"
rbd1 <- allCall.lst[[nn]]@rbd
rbd2 <- allCall.lst[[nn]]@rbd.adj
arrows <- trackBTree(btreeplotter, rbd1, rbd2, min.srcSize=0.01, 
                     min.trtSize=0.01)
btree <- drawBTree(btreeplotter, rbd1) + 
    drawBubbles(btreeplotter, rbd2, "gray80") + arrows

TrackPlotter

Description

TrackPlotter

Examples

trackplotter <- new("TrackPlotter")

vol.genes

Description

A dataset containing a list of known cancer genes.

Format

list

Source

internal

xyTrack

Description

get the xy track

Usage

xyTrack(.Object, result.dat, gr2, min.prev = 0.15, ymax = 4.3)

## S4 method for signature 'TrackPlotter'
xyTrack(.Object, result.dat, gr2, min.prev = 0.15,
  ymax = 4.3)

Arguments

.Object

the object
result.dat

result dataframe
gr2

gr2 object
min.prev

previous min
ymax

the max y

Value

the highlighted xy track

Examples

load(system.file("data", "allCall.lst.RData", package="BubbleTree"))
load(system.file("data", "centromere.dat.rda", package="BubbleTree"))
load(system.file("data", "hg19.seqinfo.rda", package="BubbleTree"))

trackplotter <- new("TrackPlotter")
gr2 = centromere.dat
nn <- "sam2"
ymax <- ifelse(nn %in% c("lung.wgs", "lung.wes"), 9, 4.3)
p1 <- xyTrack(trackplotter,
              result.dat=allCall.lst[[nn]]@result,
              gr2=gr2,
              ymax=ymax) + ggplot2::labs(title=nn)