Package 'CNViz'

Data from 2018 TCGA studies from cBioPortal

Description

A dataset containing the study name and aggregated gene level copy number data

Usage

all_tcga2018_data

Format

A data frame with 14944 rows and 6 variables:

hugoGeneSymbol

hugo gene symbol

Gain

proportion of cohort with gain in this gene

Amplification

proportion of cohort with amplification in this gene

ShallowDeletion

proportion of cohort with shallow deletion in this gene

DeepDeletion

proportion of cohort with deep deletion in this gene

study_name

cancer type and sample size

Source

https://github.com/waldronlab/cBioPortalData See data-raw folder.

---

Names of 2018 TCGA studies from cBioPortal

Description

A dataset containing the names and studyIds of the 2018 TCGA studies from cBioPortal.

Usage

cbio_studies

Format

A data frame with 32 rows and 2 variables:

Cancer

Name of diagnosis and sample size

studyId

studyId that can be used in the cBioPortalData R package

Source

https://github.com/waldronlab/cBioPortalData See data-raw folder.

---

Genomic locations of cytoband labels

Description

A dataset containing the chr, start and end position for cytobands according to hg38.

Usage

cytoband_data

Format

A data frame with 863 rows and 6 variables:

chrom

chromosome

chromStart

start position

chromEnd

end position

name

cytoband name

gieStain

color

color

HEX color

Source

https://genome.ucsc.edu/cgi-bin/hgTables

---

Gene data for vignette example

Description

A dataset containing simulated gene data as sample input for launchCNViz

Usage

data(gene_data)

Format

A dataframe with 112 rows and 6 variables

chr

chromosome

start

start location

end

end location

gene

gene name

log2

log2 copy number ratio

weight

weight given to log2 value

loh

loss of heterozygosity

Source

Center for Personalized Diagnositics at the University of Pennsylvania

---

Launches CNViz, a shiny app to visualize your sample's copy number data.

Description

CNViz launches a shiny application to visualize your sample's copy number data. At least one of probe_data, gene_data, or segment_data must be supplied; sample_name, variant_data and meta_data are all optional. The more inputs supplied, the more informative the application will be. See the CNViz vignette for more information. Use the hg38 reference genome. CNViz only displays a single sample's data.

Usage

launchCNViz(
  sample_name = "sample",
  probe_data = data.frame(),
  gene_data = data.frame(),
  segment_data = data.frame(),
  variant_data = data.frame(),
  meta_data = data.frame()
)

Arguments

sample_name	A string with the ID/name of your sample.
probe_data	A dataframe or GRanges object containing probe-level data. If a dataframe, column names must include chr, gene, start, end, log2. chr/seqnames column should be formatted as 'chr1' through 'chrX', 'chrY'. start, end and log2 should be numeric. If a GRanges object, gene and log2 are metadata columns. Optional column/metadata: weight, where weight is numeric.
gene_data	A dataframe or GRanges object containing gene-level data - one row per gene. If a dataframe, column names must include chr, gene, start, end, log2. chr/seqnames column should be formatted as 'chr1' through 'chrX', 'chrY'. start, end and log2 should be numeric. If a GRanges object, gene and log2 are metadata columns. Optional columns/metadata: weight, loh; where weight is numeric and loh values are TRUE or FALSE.
segment_data	A dataframe or GRanges object containing segment-level data. If a dataframe, column names must include chr, start, end, log2. chr column should be formatted as 'chr1' through 'chrX', 'chrY'. start, end and log2 should be numeric. If a GRanges object, log2 is a metadata column. Optional column/metadata: loh; where loh values are TRUE or FALSE.
variant_data	A dataframe or VRanges object containg SNVs and short indels and columns of your choosing. If a dataframe, the only required columns are gene and mutation_id. Optional column: start; where start indicates the starting position of the mutation. If a VRanges object, make sure gene is one of the metadata columns, so it can be tied to the gene or probe data; a mutation_id column can also be included, otherwise it will be constructed. Additional columns might include depth, allelic_fraction, ref, alt.
meta_data	A dataframe containing your sample's metadata - columns of your choosing. Optional column: ploidy; ploidy will be rounded to the nearest whole number. Additional columns might include purity. This dataframe should only have one row.

Value

a Shiny application

Examples

probes <- data.frame(chr = c("chr1", "chr1", "chr4", "chr4", "chrX"),
gene = c("NOTCH2", "NOTCH2", "KIT", "TET2", "BTK"),
start = c(119922221, 119967406,54732072,105243553,101360541),
end = c(119922461,119967646,54732192,105243793,101360781),
log2 = c(-0.0832403,-0.0578757,0.2131540,-0.3189430,-0.7876670),
weight = c(0.684114, 0.681546,0.606129,0.682368,0.405772))
segments <- data.frame(chr = c("chr1","chr1", "chr4", "chr4", "chrX"),
start = c(1050069, 124932724,   1942322,  51743951,   1198732),
end = c(122026459, 246947668,  49712061, 188110779,  37098762),
log2 = c(1, 1, 1, 1, 0.5849625), loh = c(FALSE, FALSE, FALSE, TRUE, TRUE))
meta <- data.frame(purity = c(.5),
ploidy = c(2), sex = c("Female"))

launchCNViz(sample_name = "sample123", probe_data = probes,
segment_data = segments, meta_data = meta)

---

Metadata for vignette example

Description

A dataset containing simulated metadata as sample input for launchCNViz

Usage

data(meta_data)

Format

A dataframe with 1 rows and 2 variables

purity

sample purity

ploidy

tumor ploidy

Source

Center for Personalized Diagnositics at the University of Pennsylvania

---

Probe data for vignette example

Description

A dataset containing simulated probe data as sample input for launchCNViz

Usage

data(probe_data)

Format

A data frame with 2006 rows and 6 variables:

chr

chromosome

start

start location

end

end location

gene

gene name

log2

log2 copy number ratio

weight

weight given to log2 value

Source

Center for Personalized Diagnositics at the University of Pennsylvania

---

Segment data for vignette example

Description

A dataset containing simulated segment data as sample input for launchCNViz

Usage

data(segment_data)

Format

A dataframe with 101 rows and 5 variables

chr

chromosome

start

start location

end

end location

log2

log2 copy number ratio

loh

loss of heterozygosity

Source

Center for Personalized Diagnositics at the University of Pennsylvania

---

Variant data for vignette example

Description

A dataset containing simulated SNV and indel data as sample input for launchCNViz

Usage

data(variant_data)

Format

A dataframe with 119 rows and 4 variables

gene

gene name

mutation_id

string with information about snv

depth

read depth

start

starting location

Source

Center for Personalized Diagnositics at the University of Pennsylvania

---