Deprecated

Will be merged into oncofunco package:

https://github.com/oncogenetics/oncofunco

R functions

1. SampleLocation

DNA selection from plates...

2. GeneSymbol

Collapse transcripts into gene symbols. Output is a Granges object for defined region in a chromosome.

Required packages:

require(dplyr)
require(GenomicFeatures)
require(TxDb.Hsapiens.UCSC.hg19.knownGene)
require(org.Hs.eg.db)

Example 1:

Get all genes for chr17

allGenesChr17 <- GeneSymbol(chrom = "chr17")
# Define region of interest - ROI
roi <- GRanges(seqnames="chr17",
               IRanges(start=41150000,
               end=41300000,
               names="myRegion"))
# Plot using ggbio - geom_alignment
ggplot(subsetByOverlaps(allGenesChr17,roi)) + 
  geom_alignment(aes(group=gene_id,fill=strand,col=strand))

Example 2:

Get all genes for chr17:41150000,41300000

subsetGenesChr17 <- GeneSymbol("chr17",41150000,41300000)
ggplot(subsetGenesChr17) + 
 geom_alignment(aes(group=gene_id,fill=strand,col=strand))

Plot output for Example 1 and 2

3. SNPProductRisk

Calculate Odds ratio weighted SNP risk... In progress...