SPAGMMATtest: Run single variant or gene- or region-based score tests with...
In arodri7/SAIGE-GPU: 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)

Run single variant or gene- or region-based score tests with SPA based on the linear/logistic mixed model.

SPAGMMATtest(
  bgenFile = "",
  bgenFileIndex = "",
  vcfFile = "",
  vcfFileIndex = "",
  vcfField = "DS",
  savFile = "",
  savFileIndex = "",
  sampleFile = "",
  idstoExcludeFile = "",
  idstoIncludeFile = "",
  rangestoExcludeFile = "",
  rangestoIncludeFile = "",
  chrom = "",
  start = 1,
  end = 2.5e+08,
  IsDropMissingDosages = FALSE,
  minMAC = 0.5,
  minMAF = 0,
  maxMAFforGroupTest = 0.5,
  minInfo = 0,
  GMMATmodelFile = "",
  varianceRatioFile = "",
  SPAcutoff = 2,
  SAIGEOutputFile = "",
  numLinesOutput = 10000,
  IsSparse = TRUE,
  IsOutputAFinCaseCtrl = FALSE,
  IsOutputNinCaseCtrl = FALSE,
  LOCO = FALSE,
  condition = "",
  sparseSigmaFile = "",
  groupFile = "",
  kernel = "linear.weighted",
  method = "optimal.adj",
  weights.beta.rare = c(1, 25),
  weights.beta.common = c(1, 25),
  weightMAFcutoff = 0.01,
  weightsIncludeinGroupFile = FALSE,
  weights_for_G2_cond = NULL,
  r.corr = 0,
  IsSingleVarinGroupTest = TRUE,
  cateVarRatioMinMACVecExclude = c(0.5, 1.5, 2.5, 3.5, 4.5, 5.5, 10.5, 20.5),
  cateVarRatioMaxMACVecInclude = c(1.5, 2.5, 3.5, 4.5, 5.5, 10.5, 20.5),
  dosageZerodCutoff = 0.2,
  IsOutputPvalueNAinGroupTestforBinary = FALSE,
  IsAccountforCasecontrolImbalanceinGroupTest = TRUE,
  IsOutputBETASEinBurdenTest = FALSE
)

`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 file. The file does not have a header and each line is for a marker ID.
`idstoIncludeFile`	character. Path to the file containing variant ids to be included from the bgen file. The file does not have a header and each line is for a marker ID.
`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. Note: the string needs to exactly match the chromosome string in the vcf/sav file. For example, "1" does not match "chr1". If LOCO is specified, providing chrom will save computation cost
`start`	numeric. start genome position to include from vcf file. By default, 1
`end`	numeric. end genome position to include from vcf file. By default, 250000000
`IsDropMissingDosages`	logical. whether to drop missing dosages (TRUE) or to mean impute missing dosages (FALSE). By default, FALSE. This option only works for bgen, vcf, and sav input.
`minMAC`	numeric. Minimum minor allele count of markers to test. By default, 0.5. 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 0.5.
`minInfo`	numeric. Minimum imputation info of markers to test. By default, 0. This option only works for bgen, vcf, and sav input
`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
`SPAcutoff`	by default = 2 (SPA test would be used when p value < 0.05 under the normal approximation)
`SAIGEOutputFile`	character. Path to the output file containing assoc test results
`numLinesOutput`	numeric. Number of markers to be output each time. By default, 10000
`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
`IsOutputAFinCaseCtrl`	logical. Whether to output allele frequency in cases and controls. By default, FALSE
`IsOutputNinCaseCtrl`	logical. Whether to output sample sizes in cases and controls. By default, FALSE
`LOCO`	logical. Whether to apply the leave-one-chromosome-out option. By default, FALSE
`condition`	character. For conditional analysis. Genetic marker ids (chr:pos_ref/alt if sav/vcf dosage input , marker id if bgen input) seperated by comma. e.g.chr3:101651171_C/T,chr3:101651186_G/A, Note that currently conditional analysis is only for bgen,vcf,sav input.
`sparseSigmaFile`	character. Path to the file containing the sparseSigma from step 1. The suffix of this file is ".mtx".
`groupFile`	character. Path to the file containing the group information for gene-based tests. Each line is for one gene/set of variants. The first element is for gene/set name. The rest of the line is for variant ids included in this gene/set. For vcf/sav, the genetic marker ids are in the format chr:pos_ref/alt. For bgen, the genetic marker ids should match the ids in the bgen file. Each element in the line is seperated by tab.
`kernel`	character. For gene-based test. By default, "linear.weighted". More options can be seen in the SKAT library
`method`	character. method for gene-based test p-values. By default, "optimal.adj". More options can be seen in the SKAT library
`weights.beta.rare`	vector of numeric. parameters for the beta distribution to weight genetic markers with MAF <= weightMAFcutoff in gene-based tests.By default, "c(1,25)". More options can be seen in the SKAT library
`weights.beta.common`	vector of numeric. parameters for the beta distribution to weight genetic markers with MAF > weightMAFcutoff in gene-based tests.By default, "c(1,25)". More options can be seen in the SKAT library. NOTE: this argument is not fully developed. currently, weights.beta.common is euqal to weights.beta.rare
`weightMAFcutoff`	numeric. Between 0 and 0.5. See document above for weights.beta.rare and weights.beta.common. By default, 0.01
`weightsIncludeinGroupFile`	logical. Whether to specify customized weight for makers in gene- or region-based tests. If TRUE, weights are included in the group file. For vcf/sav, the genetic marker ids and weights are in the format chr:pos_ref/alt;weight. For bgen, the genetic marker ids should match the ids in the bgen filE, e.g. SNPID;weight. Each element in the line is seperated by tab. By default, FALSE
`weights_for_G2_cond`	vector of float. weights for conditioning markers for gene- or region-based tests. The length equals to the number of conditioning markers, delimited by comma. By default, "c(1,2)"
`r.corr`	numeric. bewteen 0 and 1. parameters for gene-based tests. By default, 0. More options can be seen in the SKAT library
`IsSingleVarinGroupTest`	logical. Whether to perform single-variant assoc tests for genetic markers included in the gene-based tests. By default, FALSE
`cateVarRatioMinMACVecExclude`	vector of float. Lower bound of MAC for MAC categories. The length equals to the number of MAC categories for variance ratio estimation. By default, c(0.5,1.5,2.5,3.5,4.5,5.5,10.5,20.5). If groupFile="", only one variance ratio corresponding to MAC >= 20 is used
`cateVarRatioMaxMACVecInclude`	vector of float. Higher bound of MAC for MAC categories. The length equals to the number of MAC categories for variance ratio estimation minus 1. By default, c(1.5,2.5,3.5,4.5,5.5,10.5,20.5). If groupFile="", only one variance ratio corresponding to MAC >= 20 is used
`dosageZerodCutoff`	numeric. In gene- or region-based tests, for each variants with MAC <= 10, dosages <= dosageZerodCutoff with be set to 0. By default, 0.2.
`IsOutputPvalueNAinGroupTestforBinary`	logical. In gene- or region-based tests for binary traits. if IsOutputPvalueNAinGroupTestforBinary is TRUE, p-values without accounting for case-control imbalance will be output. By default, FALSE
`IsAccountforCasecontrolImbalanceinGroupTest`	logical. In gene- or region-based tests for binary traits. If IsAccountforCasecontrolImbalanceinGroupTest is TRUE, p-values after accounting for case-control imbalance will be output. By default, TRUE
`IsOutputBETASEinBurdenTest`	logical. Output effect size (BETA and SE) for burden tests. By default, FALSE