SCT: Stacked C+T (SCT)

In bigsnpr: Analysis of Massive SNP Arrays

Stacked C+T (SCT)

Description

Polygenic Risk Scores for a grid of clumping and thresholding parameters.

Stacking over many Polygenic Risk Scores, corresponding to a grid of many different parameters for clumping and thresholding.

Usage

snp_grid_clumping(
  G,
  infos.chr,
  infos.pos,
  lpS,
  ind.row = rows_along(G),
  grid.thr.r2 = c(0.01, 0.05, 0.1, 0.2, 0.5, 0.8, 0.95),
  grid.base.size = c(50, 100, 200, 500),
  infos.imp = rep(1, ncol(G)),
  grid.thr.imp = 1,
  groups = list(cols_along(G)),
  exclude = NULL,
  ncores = 1
)

snp_grid_PRS(
  G,
  all_keep,
  betas,
  lpS,
  n_thr_lpS = 50,
  grid.lpS.thr = 0.9999 * seq_log(max(0.1, min(lpS, na.rm = TRUE)), max(lpS, na.rm =
    TRUE), n_thr_lpS),
  ind.row = rows_along(G),
  backingfile = tempfile(),
  type = c("float", "double"),
  ncores = 1
)

snp_grid_stacking(
  multi_PRS,
  y.train,
  alphas = c(1, 0.01, 1e-04),
  ncores = 1,
  ...
)

Arguments

G	A FBM.code256 (typically ⁠<bigSNP>$genotypes⁠). You shouldn't have missing values. Also, remember to do quality control, e.g. some algorithms in this package won't work if you use SNPs with 0 MAF.
infos.chr	Vector of integers specifying each SNP's chromosome. Typically ⁠<bigSNP>$map$chromosome⁠.
infos.pos	Vector of integers specifying the physical position on a chromosome (in base pairs) of each SNP. Typically ⁠<bigSNP>$map$physical.pos⁠.
lpS	Numeric vector of -log10(p-value) associated with betas.
ind.row	An optional vector of the row indices (individuals) that are used. If not specified, all rows are used. Don't use negative indices.
grid.thr.r2	Grid of thresholds over the squared correlation between two SNPs for clumping. Default is c(0.01, 0.05, 0.1, 0.2, 0.5, 0.8, 0.95).
grid.base.size	Grid for base window sizes. Sizes are then computed as base.size / thr.r2 (in kb). Default is c(50, 100, 200, 500).
infos.imp	Vector of imputation scores. Default is all 1 if you do not provide it.
grid.thr.imp	Grid of thresholds over infos.imp (default is 1), but you should change it (e.g. c(0.3, 0.6, 0.9, 0.95)) if providing infos.imp.
groups	List of vectors of indices to define your own categories. This could be used e.g. to derive C+T scores using two different GWAS summary statistics, or to include other information such as functional annotations. Default just makes one group with all variants.
exclude	Vector of SNP indices to exclude anyway.
ncores	Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().
all_keep	Output of snp_grid_clumping() (indices passing clumping).
betas	Numeric vector of weights (effect sizes from GWAS) associated with each variant (column of G). If alleles are reversed, make sure to multiply corresponding effects by -1.
n_thr_lpS	Length for default grid.lpS.thr. Default is 50.
grid.lpS.thr	Sequence of thresholds to apply on lpS. Default is a grid (of length n_thr_lpS) evenly spaced on a logarithmic scale, i.e. on a log-log scale for p-values.
backingfile	Prefix for backingfiles where to store scores of C+T. As we typically use a large grid, this can result in a large matrix so that we store it on disk. Default uses a temporary file.
type	Type of backingfile values. Either "float" (the default) or "double". Using "float" requires half disk space.
multi_PRS	Output of snp_grid_PRS().
y.train	Vector of phenotypes. If there are two levels (binary 0/1), it uses bigstatsr::big_spLogReg() for stacking, otherwise bigstatsr::big_spLinReg().
alphas	Vector of values for grid-search. See bigstatsr::big_spLogReg(). Default for this function is c(1, 0.01, 0.0001).
...	Other parameters to be passed to bigstatsr::big_spLogReg(). For example, using covar.train, you can add covariates in the model with all C+T scores. You can also use pf.covar if you do not want to penalize these covariates.

Value

snp_grid_PRS(): An FBM (matrix on disk) that stores the C+T scores for all parameters of the grid (and for each chromosome separately). It also stores as attributes the input parameters all_keep, betas, lpS and grid.lpS.thr that are also needed in snp_grid_stacking().

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.