plinkr

Branch
`master`
`develop`

Work with PLINK and PLINK2 from R.

Doing the first PLINK example: YouTube download (.ogv)
Detect an association with one or more quantitative traits: YouTube download (.ogv)
Detect an association with ideal quantitative traits: YouTube download (.ogv)
Simulate quantitative traits: YouTube download (.ogv)
Simulate custom traits: YouTube download (.ogv)
Detect an association with a binary trait/case-control phenotype: YouTube download (.ogv)

Installation

See doc/install.md

Examples

Running PLINK

plinkr can seamlessly run any PLINK or PLINK2 versions.

Run PLINK:

library(plinkr)
run_plink("--help")

To call a specific version of PLINK:

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 :-) :

# 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

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

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.

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:

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.

File extension	`plink` read function
`.adjusted`	`read_plink_adjusted_file`
`.allele.no.snp`	🚧
`.assoc`	`read_plink_assoc_file`
`.assoc.adjusted`	`read_plink_assoc_adjusted_file`
`.assoc.dosage`	🚧
`.assoc.fisher`	🚧
`.assoc.linear`	🚧
`.assoc.logistic`	🚧
`.auto.R`	🚧
`.bcf`	🚧
`.beagle.dat`	🚧
`.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*`	🚧
`.chr-*.dat`	🚧
`.chr-*.map`	🚧
`.clst`	🚧
`.clumped*`	🚧
`.cluster*`	🚧
`.cmh`	🚧
`.cmh2`	🚧
`.cnv`	🚧
`.cnv.indiv`	🚧
`.cnv.overlap`	🚧
`.cnv.summary`	🚧
`.cov`	`read_plink_cov_file`
`.dfam`	🚧
`.diff`	🚧
`.dist`	🚧
`.dupvar`	🚧
`.eigenvec*`	🚧
`.epi.*`	🚧
`.fam`	`read_plink_fam_file`
`.flipscan`	🚧
`.frq`	`read_plink_frq_file`
`.frq.cc`	🚧
`.frq.count`	🚧
`.frq.strat`	`read_plink_frq_strat_file`
`.frqx`	🚧
`.fst`	🚧
`.gen`	🚧
`.genome`	🚧
`.grm`	🚧
`.grm.N.bin`	🚧
`.grm.bin`	🚧
`.gvar`	🚧
`.het`	🚧
`.hh`	🚧
`.hom`	🚧
`.hom.indiv`	🚧
`.hom.overlap*`	🚧
`.hom.summary`	🚧
`.homog`	🚧
`.hwe`	🚧
`.ibc`	🚧
`.imiss`	`read_plink_imiss_file`
`.info`	🚧
`.lasso`	🚧
`.ld`	`read_plink_ld_file`
`.ldset`	🚧
`.lgen`	🚧
`.list`	🚧
`.lmiss`	`read_plink_lmiss_file`
`.log`	`read_plink_log_file`
`.map`	`read_plink_map_file`
`.mdist`	🚧
`.mdist.missing`	🚧
`.mds`	🚧
`.*mendel`	🚧
`.meta`	🚧
`.mibs`	🚧
`.missing`	🚧
`.missing.hap`	🚧
`.model`	🚧
`.mperm`	🚧
`.nearest`	🚧
`.occur.dosage`	🚧
`.out.dosage`	🚧
`.ped`	`read_plink_ped_file`
`.perm`	🚧
`.phe`	`read_plink_phe_file`
`.pphe`	🚧
`.prob`	🚧
`.profile`	🚧
`.qassoc`	`read_plink_qassoc_file`
`.qassoc.gxe`	🚧
`.qassoc.means`	🚧
`.qfam.*`	🚧
`.range.report`	🚧
`.raw`	🚧
`.recode.*.txt`	🚧
`.recode.phase.inp`	🚧
`.recode.strct_in`	🚧
`.ref`	🚧
`.rel`	🚧
`.rlist`	🚧
`.sample`	🚧
`.set`	🚧
`.set.{perm,mperm}`	🚧
`.set.table`	🚧
`.sexcheck`	🚧
`.simfreq`	`read_plink_simfreq_file`
`.tags.list`	🚧
`.tdt`	🚧
`.tdt.poo`	🚧
PLINK text data	`read_plink_text_data`
`.tfam`	🚧
`.tped`	🚧
`.traw`	🚧
`.twolocus`	🚧
`.var.ranges`	🚧
`.vcf`	🚧

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` 🚧	`assoc_on_plink_text_files` 🚧
Case-control	PLINK1 bin files	`assoc` 🚧	`assoc_on_plink_bin_files` 🚧
Case-control	PLINK2 bin files	`assoc` 🚧	`assoc_on_plink2_bin_files` 🚧
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` 🚧	`assoc_qt_on_plink_text_files` 🚧
Quantitative	PLINK1 bin files	`assoc_qt` 🚧	`assoc_qt_on_plink_bin_files` 🚧
Quantitative	PLINK2 bin files	`assoc_qt` 🚧	`assoc_qt_on_plink2_bin_files` 🚧

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` 🚧
PLINK2 binary files	PLINK binary files	`convert_plink2_bin_files_to_plink_bin_files`
🚧	🚧	🚧
any type of files	PLINK text files	`convert_files_to_plink_text_files` 🚧
any type of files	PLINK1 binary files	`convert_files_to_plink_bin_files` 🚧
any type of files	PLINK2 binary files	`convert_files_to_plink2_bin_files` 🚧
PLINK1 binary files	SAIGE files	`create_bgen_files_for_saige` 🚧
PLINK1 binary files	PLINK2 VCF files	`convert_plink_bin_files_to_plink_vcf_files` 🚧

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` 🚧
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` 🚧
PLINK2 binary data	PLINK binary data	`convert_plink2_bin_data_to_plink_bin_data`

Singularity container

Find the latest ‘plinkr’ Singularity container

FAQ

See doc/faq.md

richelbilderbeek/plinkr