# Using GRangesUtilities

This package provides helpful functions for working with GRanges
objects. Start to use the package by loading it in to R

```{r}
library(GRangesUtilities)
```

This vignette will use data available in the
[VariantAnnotation](http://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html)
package. Make sure this package is installed

```{r}
pkgs <- rownames(installed.package())
stopifnot("VariantAnnotation" %in% pkgs)
```

# Utilities for VCF objects

Start by locating a sample VCF file, and reading it in to R

```{r}
fl <- system.file(package="VariantAnnotation", "extdata", 
          "chr22.vcf.gz")
vcf <- readVcf(fl, "hg19")
```

Objects input using the `readVcf` function can contain many types of
variants. Use the utility function `isSimpleVariant` to select just
those with single-character REF and ALT alleles.

```{r}
keep <- isSimpleVariant(vcf)
table(keep)
vcf <- vcf[keep]
```{r}

# Other utilities


