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Get Marginal Effects

Source: R/AllGenerics.R, R/AllClasses.R
getMarginalEffects.Rd

Extract per-variant marginal univariate effects from a fine-mapping entry or result. Returns a data.frame with identity columns (variant_id, chrom, pos, A1, A2), context (N, MAF), and the marginal effect columns (beta, se, z, p). Populated uniformly across the individual-level and RSS paths.

Usage

getMarginalEffects(x, maxPval = NULL, ...)

# S4 method for class 'FineMappingResultBase'
getMarginalEffects(
  x,
  maxPval = NULL,
  study = NULL,
  context = NULL,
  trait = NULL,
  method = NULL,
  region = NULL,
  ...
)

Arguments

x

A FineMappingRow or FineMappingResult.

maxPval

Optional numeric (length 1). When non-NULL, filter rows where p > maxPval. Default NULL (no filter).

...

Class-specific selection arguments.

study

Character (length 1) or NULL. Restrict the selection to this study; NULL matches all studies.

context

Character (length 1) or NULL. Restrict the selection to this context; NULL matches all contexts.

trait

Character (length 1) or NULL. Restrict the selection to this trait; NULL matches all traits.

method

Character (length 1) or NULL. Restrict the selection to this fine-mapping / weight method; NULL matches all methods.

region

Character (length 1, "chr:start-end") or NULL. Restrict variants to this region; NULL uses the full cis window / all regions.

Value

A data.frame.

Examples

data(qtlFineMappingExample)
getMarginalEffects(qtlFineMappingExample)
#> # A tibble: 2,828 × 16
#>    study  context trait blockId method variant_id chrom    pos A1    A2        N
#>    <chr>  <chr>   <chr> <chr>   <chr>  <chr>      <chr>  <int> <chr> <chr> <dbl>
#>  1 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 C     T       415
#>  2 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 G     T       415
#>  3 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 G     T       415
#>  4 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 C     T       415
#>  5 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 G     A       415
#>  6 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 C     T       415
#>  7 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 A     G       415
#>  8 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 G     A       415
#>  9 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 T     C       415
#> 10 study… contex… gene… NA      susie  chr22:321… chr22 3.21e7 C     A       415
#> # ℹ 2,818 more rows
#> # ℹ 5 more variables: af <dbl>, beta <dbl>, se <dbl>, z <dbl>, p <dbl>