gene_number_arm.rmd

```r
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
UCSC.hg19<- TxDb.Hsapiens.UCSC.hg19.knownGene
hg19.genes<- genes(UCSC.hg19)
transcriptsBy(UCSC.hg19, "gene")

library("org.Hs.eg.db")

## note that dplyr and AnnotationDbi both have a function called select
## use dplyr::select when use dplyr

gene_symbol<- AnnotationDbi::select(org.Hs.eg.db, keys=hg19.genes$gene_id, 
                                    columns="SYMBOL", keytype="ENTREZID")

all.equal(hg19.genes$gene_id, gene_symbol$ENTREZID)

hg19.genes$gene_id<- gene_symbol$SYMBOL

hg19.genes

## import the chrosome arm file
library(rtracklayer)
chrom.arm<- import("~/annotations/human/hg19_UCSC_genome/chrom_pq_arm.bed", format = "BED")

gene.hits<- findOverlaps(hg19.genes, chrom.arm, ignore.strand = TRUE)

queryHits(gene.hits)

## error below
genes.df <- as.data.frame(hg19.genes[queryHits(gene.hits)])

## error below
hg19.genes[queryHits(gene.hits)]$id<- chrom.arm[subjectHits(gene.hits)]$name


## one gene expands the p and q arm, suspicious https://support.bioconductor.org/p/88725/ 
## turns out this non-coding gene has two transcripts very far away.

hg19.genes[9349]

findOverlaps(hg19.genes[9349], chrom.arm)

chrom.arm[c(17,18)]

##########


### modify this gene first
hg19.genes.mod<- hg19.genes
hg19.genes.mod['286297']<- GRanges("chr9", ranges= IRanges(start = 42844370, end = 42859085), strand = "-", gene_id = "LOC286297")


gene.hits<- findOverlaps(hg19.genes.mod, chrom.arm, ignore.strand = TRUE)

queryHits(gene.hits)

genes.df <- as.data.frame(hg19.genes.mod[queryHits(gene.hits)])

genes.df$arm<- chrom.arm[subjectHits(gene.hits)]$name

library(dplyr)

gene_count_arm<- genes.df %>% group_by(seqnames, arm) %>% summarise(gene_count = n())
```