default_params_doc: This function does nothing. It is intended to inherit is...

In richelbilderbeek/plinkr: Interface to PLINK

This function does nothing. It is intended to inherit is parameters' documentation.

Description

This function does nothing. It is intended to inherit is parameters' documentation.

Usage

default_params_doc(
  add_noweb,
  allow_no_sex,
  args,
  assoc_adjusted_filename,
  assoc_data,
  assoc_filename,
  assoc_params,
  assoc_qt_covar_data,
  assoc_qt_covar_params,
  assoc_qt_data,
  assoc_qt_params,
  assoc_qt_result,
  assoc_table,
  base_input_filename,
  base_output_filename,
  base_output_plink1_filename,
  base_output_plink2_filename,
  base_phenotype_value,
  bed_filename,
  bed_table,
  bfile,
  bim_filename,
  bim_table,
  calc_phenotype_function,
  chromosome_number,
  chromosome_selector,
  confidence_interval,
  cov_filename,
  cov_table,
  data,
  eigenval_filename,
  eigenvec_filename,
  epistatic_phenotype_value,
  example_filename,
  fam_filename,
  fam_table,
  fid,
  fids,
  frq_filename,
  frq_strat_filename,
  iid,
  iids,
  ld_filename,
  ld_window_r2,
  imiss_filename,
  lmiss_filename,
  log_filename,
  maf,
  mafs,
  map_filename,
  map_table,
  n_individuals,
  n_phenotypes,
  n_samples,
  n_snps,
  n_snps_per_phenotype,
  os,
  out,
  pca_result_filenames,
  ped_filename,
  ped_table,
  pgen_filename,
  pgen_table,
  phenotype,
  phe_filename,
  phenotype_increase,
  phe_table,
  phenotypes,
  phenotype_data,
  phenotype_data_filename,
  phenotype_data_table,
  phenotype_value_dominant,
  phenotype_value_recessive,
  plink_bin_data,
  plink_bin_filenames,
  plink_exe_path,
  plink_filenames,
  plink_folder,
  plink_options,
  plink1_options,
  plink2_options,
  plink_optionses,
  plink_text_data,
  plink_text_filenames,
  plink_version,
  plink_versions,
  plinkr_folder,
  plink2_bin_data,
  plink2_bin_filenames,
  psam_filename,
  psam_table,
  pvar_filename,
  pvar_table,
  qassoc_filename,
  qassoc_filenames,
  qassoc_table,
  random_samples_selector,
  random_snps_selector,
  regular_phenotype_value,
  sample_ids,
  sample_ids_filename,
  sample_selector,
  sim_filename,
  simfreq_filename,
  simulate_qt_params,
  single_sample_selector,
  single_snp_selector,
  snp,
  snp_from,
  snp_range_selector,
  snp_selector,
  snp_to,
  snp_window_selector,
  snvs,
  temp_folder,
  temp_sim_filename,
  trait,
  traits,
  url,
  verbose,
  window_kb
)

Arguments

add_noweb	add the --noweb option, which prevents that PLINK will check if it is in its latest version. By default, this value is set to true, hence plinkr will skip this check. Use get_plink_version to get the current PLINK version.
allow_no_sex	set this to TRUE to retain phenotype values for missing-sex samples. This parameter is named after the PLINK --allow-no-sex flag
args	arguments for the PLINK or PLINK2 executable. Use check_plink_args to check if these are valid
assoc_adjusted_filename	name of a PLINK .assoc.adjusted file. Use read_plink_assoc_adjusted_file to read a PLINK .assoc.adjusted file.
assoc_data	data to use for an association analysis for a quantitative trait (i.e. using assoc), as can be created by create_assoc_data
assoc_filename	name of a PLINK .assoc file. Use read_plink_assoc_file to read a PLINK .assoc file.
assoc_params	parameters to do an association analysis for a quantitative trait (i.e. using assoc), as can be created by create_assoc_params
assoc_qt_covar_data	data to do an association analysis for a quantitative trait with covariates (i.e. using assoc_qt_covar), as can be created by create_assoc_qt_covar_data
assoc_qt_covar_params	parameters to do an association analysis for a quantitative trait with covariates (i.e. using assoc_qt_covar), as can be created by create_assoc_qt_covar_params
assoc_qt_data	data use to used by assoc_qt (as created by create_assoc_qt_data), which equals 'regular' data (see check_data) and a phenotype table/file
assoc_qt_params	parameters to do an association analysis for a quantitative trait (i.e. using assoc_qt), as can be created by create_assoc_qt_params
assoc_qt_result	the result of assoc_qt, which is a list with elements: qassoc_table: the quantitative analysis results table, as can be checked by check_qassoc_table log: the text from the log file created by PLINK/PLINK2 when doing assoc_qt
assoc_table	the table that hold the result of a case-control association, as created by PLINK/PLINK2 and stored as a .assoc file (for PLINK) or ⁠[basename].<phenotype>.[?TODO].linear⁠ (for PLINK2).
base_input_filename	the base of the filenames that are used as input for PLINK/PLINK2
base_output_filename	the base of the filenames that are used as output for PLINK/PLINK2
base_output_plink1_filename	temporary folder to create the PLINK binary files in
base_output_plink2_filename	temporary folder to create the PLINK2 binary files in
base_phenotype_value	the base phenotypic value for an additive trait, i.e. the phenotypic value for homozygotes of the common allele
bed_filename	name of a PLINK .bed file Use read_plink_bed_file to read a PLINK .bed file.
bed_table	a table that maps the SNPs to the individuals, of which the column names are the names of the individuals, the row names are the names of the SNPs, and the values are the SNP variant. Use get_test_bed_table to get a .bed table as used in testing. Use read_plink_bed_file to read a PLINK .bed file. Use check_bed_table to test if a .bed table is valid. See also the bed file format reference at https://www.cog-genomics.org/plink2/formats#bed
bfile	the base filename of the binary files (i.e. a .bed, .bim and .fam file). This parameter is named after the PLINK --bfile flag
bim_filename	name of a PLINK .bim file Use read_plink_bim_file to read a PLINK .bim file.
bim_table	a tibble of the genetic mapping, with as many rows as SNPs. Each row contains: chr: the chromosome number id: the SNP ID posg: the position pos: the position ref: something alt: something Use get_test_bim_table to get a .bim table as used in testing. Use read_plink_bim_file to read a PLINK .bim file. Use check_bim_table to test if a .bim table is valid.
calc_phenotype_function	a function that calculate the phenotypes from genotypes. The input is the genetic data as a tibble, in which each row is an individual and the columns are the SNVs. The first two columns are named snv_1a, snv_1b and hold the genetic data for the first SNV of a diploid organism. If there are more SNVs, columns continue with names, snv_2a, snv_2b, snv_3a, snv_3b, etc. Nucleotides are in uppercase. The output must be the phenotypic values, as a numeric vector, which has the same length as the number of individuals. Use check_calc_phenotype_function to check a calc_phenotype_function.
chromosome_number	the chromosome number, as can be checked by check_chromosome_number
chromosome_selector	a SNP selector (see create_snps_selector) that allows one to select a single chromsome, as created by create_chromosome_selector and checked by check_chromosome_selector
confidence_interval	confidence interval, a value between (and excluding both) 0.0 and 1.0. The confidence interval helps assess the certainty of an estimation: you can be 99 percent sure a value is within the range of the 0.99 confidence interval The confidence_interval is only used by PLINK2. For PLINK, its value is ignored
cov_filename	name of a covariates (.cov) file. Use read_plink_cov_file to read a covariates file.
cov_table	a table of covariates. A cov_table is a tibble with these columns: FID The family ID IID Within-family ID (cannot be zero) One or more columns of covariate values, columns can have any name These names match the PLINK column names (https://www.cog-genomics.org/plink/1.9/input#pheno). Use read_plink_cov_file to read a covariates file. Use check_cov_table to test if a covariates table is valid.
data	the data source, which can be: PLINK text data, as created by create_plink_text_data. PLINK binary data, as created by create_plink_bin_data. PLINK2 binary data, as created by create_plink2_bin_data. PLINK text filenames, as created by create_plink_text_filenames. PLINK binary filenames, as created by create_plink_bin_filenames. PLINK2 binary filenames, as created by create_plink2_bin_filenames. data to be used by assoc, as created by create_assoc_data data to be used by assoc_qt, as created by create_assoc_qt_data
eigenval_filename	name for a .eigenval file, as can be read with read_plink_eigenval_file
eigenvec_filename	name for a .eigenvec file, as can be read with read_plink_eigenvec_file
epistatic_phenotype_value	the phenotypic value when the epistatic phenotype is expressed
example_filename	name of the example file
fam_filename	name of a PLINK .fam file Use read_plink_fam_file to read a PLINK .fam file.
fam_table	a tibble of the genetic mapping, with as many rows as SNPs. Each row contains: fam: the family ID id: the individual's ID pat: ID of father mat: ID of mother sex: the gender pheno: a phenotype Use get_test_fam_table to get a .fam table as used in testing. Use read_plink_fam_file to read a PLINK .fam file. Use check_fam_table to test if a .fam table is valid.
fid	the family ID, which is called FID in PLINK. Use check_fid to check if a fid is valid.
fids	one or more family IDs (which are called FIDs in PLINK). Use check_fids to check if the elements of fids are valid.
frq_filename	name of a PLINK .frq file Use read_plink_frq_file to read a PLINK .frq file.
frq_strat_filename	name of a PLINK .frq.strat file Use read_plink_frq_strat_file to read a PLINK .frq.strat file.
iid	a within-family ID, as can be checked by check_iid
iids	one or more within-family IDs, as can be checked by check_iids
ld_filename	name of a PLINK/PLINK2 linkage disequilibrium (.ld) file Use read_plink_ld_file to read a PLINK .ld file.
ld_window_r2	the minimal squared correlation coefficient (also known as r^2) between markers. This parameter is named after the --ld_window_r2 flag, as documented at https://www.cog-genomics.org/plink/1.9/ld.
imiss_filename	name of a PLINK .imiss file Use read_plink_imiss_file to read a PLINK .imiss file.
lmiss_filename	name of a PLINK .lmiss file Use read_plink_lmiss_file to read a PLINK .lmiss file.
log_filename	name of a PLINK .log file
maf	minor allele frequency threshold. Alleles that have a frequency lower than the MAF are excluded from the PLINK analysis. maf must be a value between zero and 0.5 (i.e. excluding zero and excluding 0.5). By default, maf is set to the lowest representable non-zero floating-point value, as obtained by get_lowest_maf The parameter name maf is named after the PLINK --maf flag. This was chosen over more specific names such as min_allele_frequency).
mafs	one or more minor allele frequencies. These allele frequencies must be ordered decreasingly, i.e. the MAF is at the first position, where the even rarer alleles are at the second and third positions. Note that PLINK cannot handle triallelic nor quadallelic SNPs: PLINK will give a warning that it is setting the rarest alleles to missing.
map_filename	name of a PLINK .map file Use read_plink_map_file to read a PLINK .map file.
map_table	a genetic mapping table. A map_table is a tibble with the following columns: CHR: the chromosome code or contig name. The chromosome number cannot exceed 95 (https://www.cog-genomics.org/plink/1.9/input#chr_set) SNP: Variant identifier position_cm: Position in morgans or centimorgans. This value is optional. Zeroes denote it is unused BP: Base-pair coordinat Use read_plink_map_file to read a PLINK .map file. Use check_map_table to test if a genetic mapping table is valid.
n_individuals	the number of individuals. Use check_n_individuals to check if this is a valid value
n_phenotypes	the number of phenotypes
n_samples	the number of samples/individuals, as can be checked by check_n_samples
n_snps	the number of SNPs, as can be checked by check_n_snps
n_snps_per_phenotype	the number of SNPs that determine one phenotype
os	name of the operating system, as returned by app_dir
out	the base filename of the output files. This parameter is named after the PLINK --out flag
pca_result_filenames	a list with the filenames created by a call to pca
ped_filename	name of a PLINK .ped file. Use read_plink_ped_file to read a PLINK .ped file.
ped_table	a 'pedigree' table. A ped_table is a tibble with these columns: FID The family ID IID Within-family ID (cannot be zero) within_family_id_father Within-family ID of father (0 if father isn't in dataset) within_family_id_mother Within-family ID of mother (0 if mother isn't in dataset) sex_code Sex code (1 = male, 2 = female, 0 = unknown) case_control_code Case control code (1 = control, 2 = case, 9/0/non-numeric = missing data if case/control) snv_[x][y] Nucleotide for the xth variant for haplotype y (y is either a or b) in the .map file (0 = no call) The FID and IID column names match the PLINK names, see https://www.cog-genomics.org/plink/1.9/input#pheno. Use read_plink_ped_file to read a PLINK .ped file. Use check_ped_table to test if a pedigree table is valid.
pgen_filename	name of a PLINK2 .pgen file Use read_plink2_pgen_file to read a PLINK2 .pgen file
pgen_table	an array that maps the individuals to their SNPs, with as much rows as individuals, and as much SNPs as columns. Optionally, the row names are the individuals' IDs, where the column names are the SNP ID's
phenotype	one phenotype, named after its genetic background: random the phenotype is a random value, i.e. there is no association between the genetics and this phenotype additive the phenotype is perfectly additive (the nucleotides used are A and T as these are in the word 'additive'): AA 11.0 AT 10.5 TT 10.0
phe_filename	name of a phenotype (.phe) file, as checked by check_phe_filename. Use read_plink_phe_file to read a raw phenotype file.
phenotype_increase	the phenotypic value increase per rare allele, for an additive trait.
phe_table	a table of phenotypes. A phe_table is a tibble with these columns: FID The family ID IID Within-family ID (cannot be zero) One or more columns of phenotype values, columns can have any name These names match the PLINK column names (https://www.cog-genomics.org/plink/1.9/input#pheno). Use read_plink_phe_file to read a phenotype file. Use check_phe_table to test if a phenotype table is valid.
phenotypes	one ore more phenotypes, named after their genetic background: random the phenotype is a random value, i.e. there is no association between the genetics and this phenotype additive the phenotype is perfectly additive, see calc_additive_phenotype_values for the exact calculation epistatic the phenotype is epistatic, see calc_epistatic_phenotype_values for the exact calculation
phenotype_data	phenotype data in the form of either a filename to a phenotype file (phenotype_data_filename) or a list with a phenotype table (phenotype_data_table)
phenotype_data_filename	phenotype data (as checked by check_phenotype_data)) in the form of a list with a filename to a phenotype table
phenotype_data_table	phenotype data (as checked by check_phenotype_data)) in the form of a list with an in-memory phenotype table
phenotype_value_dominant	phenotypic value for the dominant variant, i.e. that genotype that has at least one version of the common common allele
phenotype_value_recessive	phenotypic value for the recessive variant, i.e. that genotype that is homozygous for the rare allele
plink_bin_data	the in-memory binary data for PLINK to work on, as created by create_plink_bin_data.
plink_bin_filenames	the binary data files' names for PLINK to work on, as created by create_plink_bin_filenames.
plink_exe_path	path to the PLINK or PLINK2 executable file.
plink_filenames	a list of filenames that is a collection of PLINK text files, PLINK binary files or PLINK2 binary files. For example, for PLINK text files, this list has elements map_filename and ped_filename
plink_folder	folder where PLINK is installed
plink_options	options to run PLINK, as created by create_plink_options
plink1_options	the PLINK version, as created by create_plink_options, for any version of PLINK
plink2_options	the PLINK2 version, as created by create_plink_options, for any version of PLINK2
plink_optionses	a list of one or more options to run PLINK, as created by create_plink_optionses. The reduplicated plural was used to express this is a list of plink_options, instead of one set of plink_options
plink_text_data	the genetic and phenotypic data for PLINK to work on, in PLINK text format, as created by create_plink_text_data.
plink_text_filenames	the text data files' names for PLINK to work on, as created by create_plink_text_filenames.
plink_version	version of PLINK, e.g. "1.7" Use get_plink_version to get the PLINK version. Use get_plink_versions to get all the supported PLINK versions.
plink_versions	one or more versions of PLINK, e.g. as can be obtained using get_plink_versions
plinkr_folder	name of the folder where plinkr stores its temporary files
plink2_bin_data	the genetic and phenotypic data for PLINK2 to work on, in PLINK2 binary format, as created by create_plink2_bin_data.
plink2_bin_filenames	the binary data files' names for PLINK2 to work on, as created by create_plink2_bin_filenames.
psam_filename	name of a PLINK2 .psam file Use read_plink2_psam_file to read a PLINK2 .psam file
psam_table	a tibble with as much rows as individuals. It has the following columns: FID: the family ID IID: the within-family ID SEX: the sex PHENO1: a phenotypic value The uppercase column names are those as used by PLINK2.
pvar_filename	name of a PLINK2 .pvar file Use read_plink2_pvar_file to read a PLINK2 .pvar file
pvar_table	a tibble with as much rows as SNPs. It has the following columns: CHROM: the chromosome POS: the position on the chromosome ID: the SNP ID REF: the reference variant ALT: the alternate variant The uppercase column names are those as used by PLINK2.
qassoc_filename	name of a PLINK .qassoc file Use read_plink_qassoc_file to read a PLINK .qassoc file.
qassoc_filenames	name of one or more PLINK .qassoc files. Use read_plink_qassoc_files to read one or more PLINK .qassoc files.
qassoc_table	the table that hold the result of an association with a quantitative trait, as created by PLINK/PLINK2 and stored as a .qassoc file (for PLINK) or ⁠[basename].<phenotype>.glm.linear⁠ (for PLINK2).
random_samples_selector	a sample selector (see create_samples_selector) that allows one to select one or more random samples, as created by create_random_samples_selector and checked by check_random_samples_selector
random_snps_selector	a SNP selector (see create_snps_selector) that allows one to select one or more random SNPs, as created by create_random_snps_selector and checked by check_random_snps_selector
regular_phenotype_value	the regular phenotypic value
sample_ids	sample IDs, which is a tibble with two columns: the first column holds the family ID (called fid or FID by PLINK/PLINK2), the second column holds the within-family ID (called iid or IID by PLINK/PLINK2), as can be checked by check_sample_ids
sample_ids_filename	name of a file to store sample_ids (see check_sample_ids) to
sample_selector	a sample/individual selector, a way to select one or more samples/individuals. See create_samples_selector for all sample selectors.
sim_filename	name of a PLINK .sim file
simfreq_filename	name of a PLINK .simfreq file
simulate_qt_params	the parameters for a quantitative traits simulation, as can be created by create_simulate_qt_params
single_sample_selector	a sample selector (see create_samples_selector for all sample selectors) that allows one to select a single sample, as created by create_single_sample_selector and checked by check_single_sample_selector
single_snp_selector	a SNP selector (see create_snps_selector for all SNP selectors) that allows one to select a single SNP, as created by create_single_snp_selector and checked by check_single_snp_selector
snp	a SNP, e.g. rs12345678, as can be checked by check_snp
snp_from	a SNP (see check_snp) to start from
snp_range_selector	a SNP selector (see create_snps_selector), that allows one to select a range between two SNPs, as created by create_snp_range_selector and checked by check_snp_range_selector
snp_selector	a SNP selector, a way to select one or more SNPs. See create_snps_selector for all SNP selectors.
snp_to	a SNP (see check_snp) to end at
snp_window_selector	a SNP selector (see create_snps_selector), that allows one to select a focal SNP and a range/window of SNPs around it, as created by create_snp_window_selector and checked by check_snp_window_selector
snvs	a tibble that contains the two nucleotide calls for multiple individuals. Each column is a haplotype, hence, for a diploid organism, there are two columns. Each individual is represented by a row. Nucleotides are in uppercase. Per SNV table, there can be only two different nucleotides, as this is how a SNP works; a SNP from A to C is a different one (and has a different SNP ID) than a SNP that encodes a mutation for A to G. Use create_snvs to create a snvs.
temp_folder	temporary folder to store results in
temp_sim_filename	temporary file to store simulation parameters, which is a PLINK .sim file
trait	one trait with a clear genetic architecture and a known minor allele frequency, as created by create_trait. Use is_one_trait to detect if something is one trait
traits	one or more traits with a clear genetic architecture and a known minor allele frequency, as, for example, created by create_demo_traits.
url	PLINK download URL
verbose	the verbosity of a function. Set to TRUE for more output. Use check_verbose to detect if this argument is valid.
window_kb	the window (i.e. the amount of base pairs around a focal SNP) in kilobases, as checked by check_window_kb

Note

This is an internal function, so it should be marked with @noRd. This is not done, as this will disallow all functions to find the documentation parameters

Author(s)

Richèl J.C. Bilderbeek

richelbilderbeek/plinkr documentation built on March 25, 2024, 3:18 p.m.