plinkr

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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