https://github.com/AJResearchGroup/plinkr

Work with PLINK from R
https://github.com/AJResearchGroup/plinkr
gwas plink plink2 r r-package
Last synced: 4 months ago
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Work with PLINK from R
Host: GitHub
URL: https://github.com/AJResearchGroup/plinkr
Owner: AJResearchGroup
License: gpl-3.0
Created: 2021-04-16T10:16:54.000Z (almost 4 years ago)
Default Branch: master
Last Pushed: 2022-06-14T14:55:40.000Z (almost 3 years ago)
Last Synced: 2024-08-13T07:13:26.215Z (8 months ago)
Topics: gwas, plink, plink2, r, r-package
Language: R
Homepage:
Size: 6.46 MB
Stars: 7
Watchers: 1
Forks: 2
Open Issues: 19
Metadata Files:
- Readme: README.Rmd
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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jimsghstars - AJResearchGroup/plinkr - Work with PLINK from R (R)
README

        ---

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "README-"

)

```

# plinkr

Branch   |[![GitHub Actions logo](man/figures/GitHubActions.png)](https://github.com/richelbilderbeek/plinkr/actions)|[![Codecov logo](man/figures/Codecov.png)](https://www.codecov.io)

---------|-----------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------

`master` |![R-CMD-check](https://github.com/richelbilderbeek/plinkr/workflows/R-CMD-check/badge.svg?branch=master)   |[![codecov.io](https://codecov.io/github/richelbilderbeek/plinkr/coverage.svg?branch=master)](https://codecov.io/github/richelbilderbeek/plinkr/branch/master)

`develop`|![R-CMD-check](https://github.com/richelbilderbeek/plinkr/workflows/R-CMD-check/badge.svg?branch=develop)  |[![codecov.io](https://codecov.io/github/richelbilderbeek/plinkr/coverage.svg?branch=develop)](https://codecov.io/github/richelbilderbeek/plinkr/branch/develop)

Work with PLINK and PLINK2 from R.

 * Doing the first PLINK example: [YouTube](https://youtu.be/LsfKQw2oIUg) [download (.ogv)](http://richelbilderbeek.nl/plinkr_basic_usage.ogv)

 * Detect an association with one or more quantitative traits: [YouTube](https://youtu.be/IicNdc8sDfI) [download (.ogv)](http://richelbilderbeek.nl/plinkr_assoc_qt.ogv)

 * Detect an association with ideal quantitative traits: [YouTube](https://youtu.be/oXGy83WiHm4) [download (.ogv)](http://richelbilderbeek.nl/plinkr_demo_qt_assoc.ogv)

 * Simulate quantitative traits: [YouTube](https://youtu.be/H0XlLVsFry4) [download (.ogv)](http://richelbilderbeek.nl/plinkr_create_demo_assoc_qt_params.ogv)

 * Simulate custom traits: [YouTube](https://youtu.be/5X1kLkiQbtw) [download (.ogv)](http://richelbilderbeek.nl/plinkr_create_custom_trait.ogv)

 * Detect an association with a binary trait/case-control phenotype: [YouTube](https://youtu.be/LhXQcDQvZS0) [download (.ogv)](http://richelbilderbeek.nl/plinkr_assoc.ogv)

## Installation

See [doc/install.md](doc/install.md)

## Examples

### Running PLINK

`plinkr` can seamlessly run any `PLINK` or `PLINK2` versions.

Run PLINK:

```{r run_plink_help, results=FALSE}

library(plinkr)

run_plink("--help")

```

To call a specific version of PLINK:

```{r run_plink_helps, results=FALSE}

run_plink(c("--help", "--noweb"), create_plink_v1_7_options())

run_plink("--help", create_plink_v1_9_options())

run_plink("--help", create_plink_v2_0_options())

```

Of course, you can also call PLINK to detect genetic associations :-) :

```{r run_plink_on_case_control_example_data, results=FALSE}

# Use the PLINK v1.9 example files

plink_v1_9 <- create_plink_v1_9_options()

ped_filename <- get_plink_example_filename("toy.ped", plink_v1_9)

map_filename <- get_plink_example_filename("toy.map", plink_v1_9)

# Do a case-control association

plinkr::run_plink(

  args = c(

    "--ped", ped_filename, 

    "--map", map_filename

  )

)

```

 * See the vignette `basic_usage` for basic usage of PLINK, 

   as taken from the PLINK website, which shows a 

   quantitative trait analysis

 * See the vignette `test_assoc_qt` for the same basic usage of PLINK,

   using the `plinkr` interface

 * See the vignette `demo_assoc_qt` for doing a quantitative trait

   analysis using simulated data and the `plinkr` interface

### Run a quantitative trait analysis on existing files

#### Read from PLINK text files

```{r run_assoc_plink_text_files, results=FALSE}

assoc_qt_data <- create_assoc_qt_data(

  data = create_plink_text_filenames(

    map_filename = get_plinkr_filename("demo_assoc_qt.map"), 

    ped_filename = get_plinkr_filename("demo_assoc_qt.ped")

  ),

  phenotype_data = create_phenotype_data_filename(

    phe_filename = get_plinkr_filename("demo_assoc_qt.phe")  

  )

)

assoc_qt_filenames <- assoc_qt(assoc_qt_data = assoc_qt_data)

read_plink_qassoc_file(assoc_qt_filenames$qassoc_filenames[1])

```

#### Read from PLINK binary files

```{r run_assoc_plink_bin_files, results=FALSE}

assoc_qt_data <- create_assoc_qt_data(

  data = create_plink_bin_filenames(

    bed_filename = get_plinkr_filename("demo_assoc_qt.bed"), 

    bim_filename = get_plinkr_filename("demo_assoc_qt.bim"), 

    fam_filename = get_plinkr_filename("demo_assoc_qt.fam")

  ),

  phenotype_data = create_phenotype_data_filename(

    phe_filename = get_plinkr_filename("demo_assoc_qt.phe")  

  )

)

assoc_qt_filenames <- assoc_qt(assoc_qt_data = assoc_qt_data)

read_plink_qassoc_file(assoc_qt_filenames$qassoc_filenames[1])

```

### Demonstrate a quantitative trait analysis

`plinkr` can seamlessly use `PLINK`/`PLINK2` in-memory-data or files.

```{r run_assoc_qt_plink_text_data, results=FALSE}

assoc_qt_data <- create_demo_assoc_qt_data()

# Prove that this is PLINK text data

check_plink_text_data(assoc_qt_data$data)

assoc_qt_params <- create_test_assoc_qt_params()

assoc_qt(

  assoc_qt_data = assoc_qt_data,

  assoc_qt_params = assoc_qt_params

)

```

To convert the in-memory data to PLINK binary format and do the same

quantitative trait analysis:

```{r run_assoc_qt_plink_bin_data, results=FALSE}

assoc_qt_data$data <- convert_plink_text_data_to_plink_bin_data(

  assoc_qt_data$data

)

# Prove that this is PLINK binary data

check_plink_bin_data(assoc_qt_data$data)

assoc_qt(

  assoc_qt_data = assoc_qt_data,

  assoc_qt_params = assoc_qt_params

)

```

 * See the vignette `demo_assoc_qt` for a walk-through of

   the data that is simulated by default

 * See the vignette `create_demo_assoc_qt_params` for many

   examples how data can be simulated

### File I/O

`plinkr` can read and save many types of PLINK files.

Below is an overview. 

List from [the PLINK file format reference](https://www.cog-genomics.org/plink2/formats).

File extension      |`plink` read function

--------------------|--------------------------

`.adjusted`         |`read_plink_adjusted_file`

`.allele.no.snp`    |:construction: 

`.assoc`            |`read_plink_assoc_file`

`.assoc.adjusted`   |`read_plink_assoc_adjusted_file`

`.assoc.dosage`     |:construction: 

`.assoc.fisher`     |:construction: 

`.assoc.linear`     |:construction: 

`.assoc.logistic`   |:construction: 

`.auto.R`           |:construction: 

`.bcf`              |:construction: 

`.beagle.dat`       |:construction:

`.bed`              |`read_plink_bed_file`

`.bim`              |`read_plink_bin_file`

PLINK binary data   |`read_plink_bin_data`

PLINK2 binary data  |`read_plink2_bin_data`

`.blocks*`          |:construction: 

`.chr-*.dat`        |:construction: 

`.chr-*.map`        |:construction: 

`.clst`             |:construction: 

`.clumped*`         |:construction: 

`.cluster*`         |:construction: 

`.cmh`              |:construction: 

`.cmh2`             |:construction: 

`.cnv`              |:construction: 

`.cnv.indiv`        |:construction: 

`.cnv.overlap`      |:construction: 

`.cnv.summary`      |:construction: 

`.cov`              |`read_plink_cov_file`

`.dfam`             |:construction: 

`.diff`             |:construction: 

`.dist`             |:construction:

`.dupvar`           |:construction: 

`.eigenval`         |`read_plink_eigenval_file`

`.eigenvec`         |`read_plink_eigenvec_file`

`.eigenvec*`        |:construction:

`.epi.*`            |:construction:

`.fam`              |`read_plink_fam_file` 

`.flipscan`         |:construction: 

`.frq`              |`read_plink_frq_file` 

`.frq.cc`           |:construction: 

`.frq.count`        |:construction: 

`.frq.strat`        |`read_plink_frq_strat_file` 

`.frqx`             |:construction: 

`.fst`              |:construction: 

`.gen`              |:construction: 

`.genome`           |:construction: 

`.grm`              |:construction: 

`.grm.N.bin`        |:construction: 

`.grm.bin`          |:construction: 

`.gvar`             |:construction: 

`.het`              |:construction: 

`.hh`               |:construction: 

`.hom`              |:construction: 

`.hom.indiv`        |:construction:

`.hom.overlap*`     |:construction: 

`.hom.summary`      |:construction: 

`.homog`            |:construction: 

`.hwe`              |:construction: 

`.ibc`              |:construction: 

`.imiss`            |`read_plink_imiss_file` 

`.info`             |:construction: 

`.lasso`            |:construction: 

`.ld`               |`read_plink_ld_file` 

`.ldset`            |:construction: 

`.lgen`             |:construction: 

`.list`             |:construction: 

`.lmiss`            |`read_plink_lmiss_file` 

`.log`              |`read_plink_log_file` 

`.map`              |`read_plink_map_file` 

`.mdist`            |:construction: 

`.mdist.missing`    |:construction: 

`.mds`              |:construction: 

`.*mendel`          |:construction: 

`.meta`             |:construction: 

`.mibs`             |:construction: 

`.missing`          |:construction: 

`.missing.hap`      |:construction: 

`.model`            |:construction: 

`.mperm`            |:construction: 

`.nearest`          |:construction: 

`.occur.dosage`     |:construction: 

`.out.dosage`       |:construction: 

`.ped`              |`read_plink_ped_file` 

`.perm`             |:construction: 

`.phe`              |`read_plink_phe_file` 

`.pphe`             |:construction: 

`.prob`             |:construction: 

`.profile`          |:construction: 

`.qassoc`           |`read_plink_qassoc_file` 

`.qassoc.gxe`       |:construction: 

`.qassoc.means`     |:construction: 

`.qfam.*`           |:construction: 

`.range.report`     |:construction: 

`.raw`              |:construction: 

`.recode.*.txt`     |:construction: 

`.recode.phase.inp` |:construction: 

`.recode.strct_in`  |:construction: 

`.ref`              |:construction: 

`.rel`              |:construction: 

`.rlist`            |:construction: 

`.sample`           |:construction: 

`.set`              |:construction: 

`.set.{perm,mperm}` |:construction: 

`.set.table`        |:construction: 

`.sexcheck`         |:construction: 

`.simfreq`          |`read_plink_simfreq_file` 

`.tags.list`        |:construction: 

`.tdt`              |:construction: 

`.tdt.poo`          |:construction: 

PLINK text data     |`read_plink_text_data`

`.tfam`             |:construction: 

`.tped`             |:construction: 

`.traw`             |:construction: 

`.twolocus`         |:construction: 

`.var.ranges`       |:construction: 

`.vcf`              |:construction:

### Associations

Association type|Data type        |General function          |Specialized function

----------------|-----------------|--------------------------|------------------------------------------

Case-control    |PLINK1 text data |`assoc`                   |`assoc_on_plink_text_data`

Case-control    |PLINK1 bin data  |`assoc`                   |`assoc_on_plink_bin_data`

Case-control    |PLINK2 bin data  |`assoc`                   |`assoc_on_plink2_bin_data`

Case-control    |PLINK1 text files|`assoc` :construction:    |`assoc_on_plink_text_files` :construction:

Case-control    |PLINK1 bin files |`assoc` :construction:    |`assoc_on_plink_bin_files` :construction:

Case-control    |PLINK2 bin files |`assoc` :construction:    |`assoc_on_plink2_bin_files` :construction:

Quantitative    |PLINK1 text data |`assoc_qt`                |`assoc_qt_on_plink_text_data`

Quantitative    |PLINK1 bin data  |`assoc_qt`                |`assoc_qt_on_plink_bin_data`

Quantitative    |PLINK2 bin data  |`assoc_qt`                |`assoc_qt_on_plink2_bin_data`

Quantitative    |PLINK1 text files|`assoc_qt` :construction: |`assoc_qt_on_plink_text_files` :construction:

Quantitative    |PLINK1 bin files |`assoc_qt` :construction: |`assoc_qt_on_plink_bin_files` :construction:

Quantitative    |PLINK2 bin files |`assoc_qt` :construction: |`assoc_qt_on_plink2_bin_files` :construction:

### PLINK and PLINK2 files conversions

`plinkr` allows to convert between any PLINK and PLINK2 files.

From               |To                 |Function name

-------------------|-------------------|----------------------------------------------

PLINK1 text files  |PLINK1 binary files|`convert_plink_text_files_to_plink_bin_files`

PLINK1 text files  |PLINK2 binary files|`convert_plink_text_files_to_plink2_bin_files`

PLINK1 binary files|PLINK text files   |`convert_plink_bin_files_to_plink_text_files`

PLINK1 binary files|PLINK2 binary files|`convert_plink_bin_files_to_plink2_bin_files`

PLINK2 binary files|PLINK text files   |`convert_plink2_bin_files_to_plink_text_files` :construction:

PLINK2 binary files|PLINK binary files |`convert_plink2_bin_files_to_plink_bin_files`

:construction:     |:construction:     |:construction:

any type of files  |PLINK text files   |`convert_files_to_plink_text_files` :construction:

any type of files  |PLINK1 binary files|`convert_files_to_plink_bin_files` :construction:

any type of files  |PLINK2 binary files|`convert_files_to_plink2_bin_files` :construction:

PLINK1 binary files|SAIGE files        |`create_bgen_files_for_saige` :construction:

PLINK1 binary files|PLINK2 VCF files   |`convert_plink_bin_files_to_plink_vcf_files` :construction:

### PLINK and PLINK2 data conversions

`plinkr` allows to convert between any PLINK and PLINK2 data.

From              |To                |Function name

------------------|------------------|--------------------------------------------

PLINK1 text data  |PLINK1 binary data|`convert_plink_text_data_to_plink_bin_data`

PLINK1 text data  |PLINK2 binary data|`convert_plink_text_data_to_plink2_bin_data`

PLINK1 binary data|PLINK text data   |`convert_plink_bin_data_to_plink_text_data` :construction:

PLINK1 binary data|PLINK2 binary data|`convert_plink_bin_data_to_plink2_bin_data`

PLINK2 binary data|PLINK text data   |`convert_plink2_bin_data_to_plink_text_data` :construction:

PLINK2 binary data|PLINK binary data |`convert_plink2_bin_data_to_plink_bin_data`

## Singularity container

 * [Find the latest 'plinkr' Singularity container](https://cloud.sylabs.io/library/search;query=plinkr)

## FAQ

See [doc/faq.md](doc/faq.md)
ecosyste.ms

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README
