subset.Rmd

---
title: "Subsetting PyRanges"
---

# Subsetting PyRanges

There are many ways to subset a PyRanges object. Each returns a new PyRanges object and does not change the old one.

```{python}

import pyranges as pr

gr = pr.load_dataset("chipseq")
print(gr)
```


Chromosome only


```{python tidy=FALSE}

print(gr["chrX"])
```

Chromosome and Strand


```{python tidy=FALSE}

print(gr["chrX", "-"])
```

Chromosome and Slice


```{python tidy=FALSE}

print(gr["chrX", 150000000:160000000])
```

Chromosome, Strand and Slice


```{python tidy=FALSE}

print(gr["chrX", "-", 150000000:160000000])
```

Slice

Only using slices returns all ranges from all chromosomes and strands within those coordinates.

```{python tidy=FALSE}

print(gr[0:100000])
```

Strand


```{python tidy=FALSE}

print(gr["+"])
```

Slice and Strand


```{python tidy=FALSE}

print(gr["+", 0:100000])
```