target_cnv_calls: CNV calls, corrected for purity

Description Usage Value Examples

View source: R/target_cnv_purity_corrected_calls.R

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

1

Value

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

Examples

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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 Aug. 15, 2019, 5:12 p.m.