SKATtest_usingSKATLib: Run single variant score tests with SPA based on the logistic...
In weizhouUMICH/SAIGE: Efficiently controlling for case-control imbalance and sample relatedness in single-variant assoc tests (SAIGE) and controlling for sample relatedness in region-based assoc tests in large cohorts and biobanks (SAIGE-GENE)

View source: R/SAIGE_SKAT_NULL_Model_usingSKATLib_p.R

SKATtest_usingSKATLib

R Documentation

Run single variant score tests with SPA based on the logistic mixed model.

Description

Run single variant score tests with SPA based on the logistic mixed model.

Usage

SKATtest_usingSKATLib(
  dosageFile = "",
  dosageFileNrowSkip = 0,
  dosageFileNcolSkip = 0,
  dosageFilecolnamesSkip = c("SNPID", "CHR", "POS", "Allele0", "Allele1"),
  dosageFileChrCol = "CHR",
  bgenFile = "",
  bgenFileIndex = "",
  vcfFile = "",
  vcfFileIndex = "",
  vcfField = "DS",
  savFile = "",
  savFileIndex = "",
  sampleFile = "",
  idstoExcludeFile = "",
  idstoIncludeFile = "",
  rangestoExcludeFile = "",
  rangestoIncludeFile = "",
  chrom = "",
  start = 1,
  end = 2.5e+08,
  minMAC = 0.5,
  minMAF = 0,
  maxMAFforGroupTest = 1,
  minInfo = 0,
  SKATmodelFile = "",
  SAIGEOutputFile = "",
  numLinesOutput = 10000,
  IsOutputAFinCaseCtrl = FALSE,
  groupFile = "",
  condition = "",
  kernel = "linear.weighted",
  method = "optimal.adj",
  weights.beta = c(1, 25),
  r.corr = 0
)

Arguments

`dosageFile`	character. Path to dosage file. Each line contains dosages for a marker to be tested
`dosageFileNrowSkip`	integer(>=0). Number of lines to be skiped in the dosage file.
`dosageFileNcolSkip`	integer(>=0). Number of columns to be skiped in the dosage file
`dosageFilecolnamesSkip`	vector of characters. The column names of the skipped columns. Default: c("SNPID", "CHR", "POS", "Allele0", "Allele1")
`dosageFileChrCol`	string. The column name for the chromosome column. Must be in the dosageFilecolnamesSkip. Required If LOCO = TRUE and chrom ="".
`bgenFile`	character. Path to bgen file. Currently version 1.2 with 8 bit compression is supported
`bgenFileIndex`	character. Path to the .bgi file (index of the bgen file)
`vcfFile`	character. Path to vcf file
`vcfFileIndex`	character. Path to index for vcf file by tabix, ".tbi" by "tabix -p vcf file.vcf.gz"
`vcfField`	character. genotype field in vcf file to use. "DS" for dosages or "GT" for genotypes. By default, "DS".
`savFile`	character. Path to sav file
`savFileIndex`	character. Path to index for sav file .s1r
`sampleFile`	character. Path to the file that contains one column for IDs of samples in the dosage, vcf, sav, or bgen file with NO header
`idstoExcludeFile`	character. Path to the file containing variant ids to be excluded from the bgen or vcf file
`idstoIncludeFile`	character. Path to the file containing variant ids to be included from the bgen or vcf file
`rangestoExcludeFile`	character. Path to the file containing genome regions to be excluded from the bgen file. The file contains three columns for chromosome, start, and end respectively with no header
`rangestoIncludeFile`	character. Path to the file containing genome regions to be included from the bgen file. The file contains three columns for chromosome, start, and end respectively with no header
`chrom`	character. string for the chromosome to include from vcf file. Required for vcf file. If LOCO is specified, providing chrom will save computation cost
`start`	numeric. start genome position to include from vcf file.
`end`	numeric. end genome position to include from vcf file.
`minMAC`	numeric. Minimum minor allele count of markers to test. By default, 1. The higher threshold between minMAC and minMAF will be used
`minMAF`	numeric. Minimum minor allele frequency of markers to test. By default 0. The higher threshold between minMAC and minMAF will be used
`maxMAFforGroupTest`	numeric. Maximum minor allele frequency of markers to test in group test. By default 1.
`minInfo`	numeric. Minimum imputation info of markers to test (in bgen file)
`SAIGEOutputFile`	character. Path to the output file containing the SPAGMMAT test results
`numLinesOutput`	numeric. Output results for how many marker each time.
`IsOutputAFinCaseCtrl`	logical. Whether to output allele frequency in cases and controls. By default, FALSE
`groupFile`	character. Path to the group file containing one column "GeneID", and one column for ID of the tested genetic markers delimited by comma. This file is space-delimited can only work with the bgen,sav,and vcf format
`GMMATmodelFile`	character. Path to the input file containing the glmm model, which is output from previous step. Will be used by load()
`varianceRatioFile`	character. Path to the input file containing the variance ratio, which is output from the previous step
`Cutoff`	by default = 2 (SPA test would be used when p value < 0.05 under the normal approximation)
`IsSparse`	logical. Whether to exploit the sparsity of the genotype vector for less frequent variants to speed up the SPA tests or not for dichotomous traits. By default, TRUE
`condition.`	For conditional analysis. Genetic marker ids (chr:pos_ref/alt) seperated by comma. e.g.chr3:101651171_C/T,chr3:101651186_G/A. Note that currently conditional analysis is only for vcf/sav input.