In richelbilderbeek/plinkr: Interface to PLINK

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

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 |: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