target_cnv_calls: CNV calls, corrected for purity

In seandavi/TargetOsteoAnalysis: Access Open-access TARGET Osteosarcoma Data

Description

This function loads the pureCN-corrected copy number data as generated by cnvKit call. The data were accessed from /data/CCRBioinfo/projects/TargetOsteoDiscovery/report/summary.pureCN.cns.calls on December 13, 2018.

Usage

target_cnv_calls()

Value

A GRanges object describing regions of copy number change with medata columns:

• log2: log2 copy number

• baf: average B-Allele-Frequency for the copy number region

• cn: total integer copy number

• cn1: integer copy number of allele 1

• cn2: integer copy number of allele 2

• depth: average depth of region

• probes: from cnvKit, the number of bins

• weight: from cnvKit

Examples

x = target_cnv_calls()
head(x)
colnames(x)
# number of regions per sample
hist(as.vector(table(x$sampleName)))
hist(x$baf)
hist(x$log2)

# Make a plot of log2 vs BAF for TP53 gene
## Not run: 
library(GenomicRanges)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
glocs = genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
library(AnnotationDbi)
glocs$symbol = unlist(AnnotationDbi::select(org.Hs.eg.db,
    columns = "SYMBOL", keytype = "ENTREZID", keys = glocs$gene_id)$SYMBOL)
glocs = glocs[!is.na(glocs$symbol)]
tp53_regions = subsetByOverlaps(x, glocs[glocs$symbol=='TP53'])
plot(tp53_regions$log2, tp53_regions$baf)

## End(Not run)

seandavi/TargetOsteoAnalysis documentation built on May 22, 2020, 8:23 p.m.