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https://github.com/const-ae/tidygenomics
Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/
https://github.com/const-ae/tidygenomics
genomics intervals r-package r-stats tidy
Last synced: about 2 months ago
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Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/
- Host: GitHub
- URL: https://github.com/const-ae/tidygenomics
- Owner: const-ae
- Created: 2017-05-07T20:45:40.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2021-04-15T07:00:02.000Z (over 3 years ago)
- Last Synced: 2024-10-28T17:32:31.708Z (about 2 months ago)
- Topics: genomics, intervals, r-package, r-stats, tidy
- Language: R
- Homepage:
- Size: 206 KB
- Stars: 102
- Watchers: 4
- Forks: 5
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# tidygenomics
[](https://cran.r-project.org/package=tidygenomics)
Tidy Verbs for Dealing with Genomic Data Frames
## Description
Handle genomic data within data frames just as you would with `GRanges`.
This packages provides method to deal with genomics intervals the "tidy-way" which makes
it simpler to integrate in the the general data munging process. The API is inspired by the
popular bedtools and the genome_join() method from the fuzzyjoin package.
## Installation
```
install.packages("tidygenomics")
```
Or to get the latest development version
```
devtools::install_github("const-ae/tidygenomics")
```
## Documentation
#### genome_intersect
Joins 2 data frames based on their genomic overlap. Unlike the `genome_join` function it updates the boundaries to reflect
the overlap of the regions.
```{r}
x1 <- data.frame(id = 1:4,
chromosome = c("chr1", "chr1", "chr2", "chr2"),
start = c(100, 200, 300, 400),
end = c(150, 250, 350, 450))
x2 <- data.frame(id = 1:4,
chromosome = c("chr1", "chr2", "chr2", "chr1"),
start = c(140, 210, 400, 300),
end = c(160, 240, 415, 320))
genome_intersect(x1, x2, by=c("chromosome", "start", "end"), mode="both")
```
| id.x|chromosome | id.y| start| end|
|----:|:----------|----:|-----:|---:|
| 1|chr1 | 1| 140| 150|
| 4|chr2 | 3| 400| 415|
#### genome_subtract
Subtracts one data frame from the other. This can be used to split the x data frame into smaller areas.
```{r}
x1 <- data.frame(id = 1:4,
chromosome = c("chr1", "chr1", "chr2", "chr1"),
start = c(100, 200, 300, 400),
end = c(150, 250, 350, 450))
x2 <- data.frame(id = 1:4,
chromosome = c("chr1", "chr2", "chr1", "chr1"),
start = c(120, 210, 300, 400),
end = c(125, 240, 320, 415))
genome_subtract(x1, x2, by=c("chromosome", "start", "end"))
```
| id|chromosome | start| end|
|--:|:----------|-----:|---:|
| 1|chr1 | 100| 119|
| 1|chr1 | 126| 150|
| 2|chr1 | 200| 250|
| 3|chr2 | 300| 350|
| 4|chr1 | 416| 450|
#### genome_join_closest
Joins 2 data frames based on their genomic location. If no exact overlap is found the next closest interval is used.
```{r}
x1 <- data_frame(id = 1:4,
chr = c("chr1", "chr1", "chr2", "chr3"),
start = c(100, 200, 300, 400),
end = c(150, 250, 350, 450))
x2 <- data_frame(id = 1:4,
chr = c("chr1", "chr1", "chr1", "chr2"),
start = c(220, 210, 300, 400),
end = c(225, 240, 320, 415))
genome_join_closest(x1, x2, by=c("chr", "start", "end"), distance_column_name="distance", mode="left")
```
| id.x|chr.x | start.x| end.x| id.y|chr.y | start.y| end.y| distance|
|----:|:-----|-------:|-----:|----:|:-----|-------:|-----:|--------:|
| 1|chr1 | 100| 150| 2|chr1 | 210| 240| 59|
| 2|chr1 | 200| 250| 1|chr1 | 220| 225| 0|
| 2|chr1 | 200| 250| 2|chr1 | 210| 240| 0|
| 3|chr2 | 300| 350| 4|chr2 | 400| 415| 49|
| 4|chr3 | 400| 450| NA|NA | NA| NA| NA|
#### genome_cluster
Add a new column with the cluster if 2 intervals are overlapping or are within the `max_distance`.
```{r}
x1 <- data.frame(id = 1:4, bla=letters[1:4],
chromosome = c("chr1", "chr1", "chr2", "chr1"),
start = c(100, 120, 300, 260),
end = c(150, 250, 350, 450))
genome_cluster(x1, by=c("chromosome", "start", "end"))
```
| id|bla |chromosome | start| end| cluster_id|
|--:|:---|:----------|-----:|---:|----------:|
| 1|a |chr1 | 100| 150| 0|
| 2|b |chr1 | 120| 250| 0|
| 3|c |chr2 | 300| 350| 2|
| 4|d |chr1 | 260| 450| 1|
```{r}
genome_cluster(x1, by=c("chromosome", "start", "end"), max_distance=10)
```
| id|bla |chromosome | start| end| cluster_id|
|--:|:---|:----------|-----:|---:|----------:|
| 1|a |chr1 | 100| 150| 0|
| 2|b |chr1 | 120| 250| 0|
| 3|c |chr2 | 300| 350| 1|
| 4|d |chr1 | 260| 450| 0|
#### genome_complement
Calculates the complement of a genomic region.
```{r}
x1 <- data.frame(id = 1:4,
chromosome = c("chr1", "chr1", "chr2", "chr1"),
start = c(100, 200, 300, 400),
end = c(150, 250, 350, 450))
genome_complement(x1, by=c("chromosome", "start", "end"))
```
|chromosome | start| end|
|:----------|-----:|---:|
|chr1 | 1| 99|
|chr1 | 151| 199|
|chr1 | 251| 399|
|chr2 | 1| 299|
#### genome_join
Classical join function based on the overlap of the interval. Implemented and maintained in the
[fuzzyjoin](https://github.com/dgrtwo/fuzzyjoin) package and documented here only for completeness.
```{r}
x1 <- data_frame(id = 1:4,
chr = c("chr1", "chr1", "chr2", "chr3"),
start = c(100, 200, 300, 400),
end = c(150, 250, 350, 450))
x2 <- data_frame(id = 1:4,
chr = c("chr1", "chr1", "chr1", "chr2"),
start = c(220, 210, 300, 400),
end = c(225, 240, 320, 415))
fuzzyjoin::genome_join(x1, x2, by=c("chr", "start", "end"), mode="inner")
```
| id.x|chr.x | start.x| end.x| id.y|chr.y | start.y| end.y|
|----:|:-----|-------:|-----:|----:|:-----|-------:|-----:|
| 2|chr1 | 200| 250| 1|chr1 | 220| 225|
| 2|chr1 | 200| 250| 2|chr1 | 210| 240|
```{r}
fuzzyjoin::genome_join(x1, x2, by=c("chr", "start", "end"), mode="left")
```
| id.x|chr.x | start.x| end.x| id.y|chr.y | start.y| end.y|
|----:|:-----|-------:|-----:|----:|:-----|-------:|-----:|
| 1|chr1 | 100| 150| NA|NA | NA| NA|
| 2|chr1 | 200| 250| 1|chr1 | 220| 225|
| 2|chr1 | 200| 250| 2|chr1 | 210| 240|
| 3|chr2 | 300| 350| NA|NA | NA| NA|
| 4|chr3 | 400| 450| NA|NA | NA| NA|
```{r}
fuzzyjoin::genome_join(x1, x2, by=c("chr", "start", "end"), mode="anti")
```
| id|chr | start| end|
|--:|:----|-----:|---:|
| 1|chr1 | 100| 150|
| 3|chr2 | 300| 350|
| 4|chr3 | 400| 450|
## Inspiration
- [tidyverse](http://tidyverse.org/)
- [fuzzyjoin](https://github.com/dgrtwo/fuzzyjoin)
- [GenomicRanges](http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html)
- [bedtools](http://bedtools.readthedocs.io)
If you have any additional questions or encounter issues please raise them on the [github page](https://github.com/Artjom-Metro/tidygenomics).