tile bed file to same width bins

tile_bed_file_to_bins.rmd

Note, bed file is 0-based, and R is 1 based. when import bed file to
R, the GRanges will add 1 in the start.

cat test.bed

chr1 1 14
chr1 14 20
chr1 30 38

```{r}
library(GenomicRanges)
library(rtracklayer)
library(dplyr)
library(readr)


gr<- import("~/playground/test.bed")
bin_size<- 5

gr_width<- width(gr)
bin_num<- ceiling(gr_width/bin_size)

## after extending, the peaks are overlapping
gr_center<- resize(gr, fix = "center", width = bin_num * bin_size)


## this works fine
unlist(tile(gr_center, width = bin_size))

## merge before tile
gr_center_merge<- reduce(gr_center)

out_bed<- unlist(tile(gr_center_merge, width = bin_size))

## trim the out of bound gr
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txdb<- TxDb.Hsapiens.UCSC.hg38.knownGene
seqinfo(out_bed)<- seqinfo(txdb)
out_bed<- trim(out_bed)


## will handle the bed format: -1 at the start, but the output will be 6-column bed
export(out_bed, "~/playground/out.bed", format = "BED")

# or
out_bed %>% as.data.frame() %>%
mutate(start = start -1) %>%
dplyr::select(seqnames, start, end) %>%
write_tsv("~/playground/out2.bed", col_names = FALSE)
```