Package 'mrSampleOverlap'

Title: Estimate Bias Due To Sample Overlap In Mendelian Randomization Studies
Description: A function to estimate bias due to sample overlap in Mendelian Randomization studies.
Authors: Michael Levin [aut, cre]
Maintainer: Michael Levin <[email protected]>
License: MIT + file LICENSE
Version: 0.1.1
Built: 2025-01-01 04:20:51 UTC
Source: https://github.com/mglev1n/mrSampleOverlap

Help Index

Estimate F-statistic

Description

Estimate F-statistic

Usage

estimate_f(samplesize_exposure, n_variants, rsq_exposure, lci_95 = FALSE)

Arguments

samplesize_exposure

(numeric) Sample size of population used to define genetic instrument for the exposure of interest
n_variants

(numeric) Number of genetic variants included in genetic instrument for the exposure of interest
rsq_exposure

(numeric) R2R^2 value (coefficient of determination) of genetic instrument for the exposure of interest; used to estimate
lci_95

(logical; default = FALSE) If TRUE, the function will return the lower limit of the one-sided 95% confidence interval of the F-statistic, which may represent a more conservative/less optimistic estimate

Value

Numeric vector containing the estimated F-statistic

Examples

estimate_f(samplesize_exposure = 361194, n_variants = 196, rsq_exposure = 0.068, lci_95 = FALSE)

# return lower bound of one-sided 95% confidence interval of F-statistic
estimate_f(samplesize_exposure = 361194, n_variants = 196, rsq_exposure = 0.068, lci_95 = TRUE)

Estimate bias due to sample overlap

Description

Estimate bias due to sample overlap

Usage

estimate_overlap_bias(
  samplesize_exposure,
  samplesize_outcome,
  n_variants,
  rsq_exposure,
  exp_f = NULL,
  lci_95 = FALSE,
  case_prop = 0,
  ols_bias,
  overlap_prop,
  var_x = 1,
  var_y = 1
)

Arguments

samplesize_exposure

(numeric) Sample size of population used to define genetic instrument for the exposure of interest
samplesize_outcome

(numeric) Sample size of population used for the outcome of interest
n_variants

(numeric) Number of genetic variants included in genetic instrument for the exposure of interest
rsq_exposure

(numeric) R2R^2 value (coefficient of determination) of genetic instrument for the exposure of interest; used to estimate F-statistic
exp_f

(numeric; optional) F-statistic for the genetic instrument (if provided, this value will be used, rather than an estimate based on the R2R^2)
lci_95

(logical; default = FALSE) If TRUE, the function will return estimates of bias and type 1 error based on the lower limit of the one-sided 95% confidence interval of the F-statistic, which may represent a more conservative/less optimistic estimate of bias
case_prop

(numeric; optional) Proportion of cases (eg. cases/total samplesize) if outcome is binary
ols_bias

(numeric) Observational (biased) effect estimate (if known); otherwise, provide a hypothetical value
overlap_prop

(numeric; range = 0 to 1) Proportion of overlapping samples between exposure and outcome studies (if known); otherwise, provide a hypothetical value
var_x

(numeric) Variance in the exposure; default is 1 when the exposure is reported in standard deviation units
var_y

(numeric) Variance in the exposure; default is 1 when the exposure is reported in standard deviation units

Value

A tibble containing columns for the bias and type1_error

Examples

# Binary outcome
estimate_overlap_bias(
  samplesize_exposure = 361194,
  samplesize_outcome = 1125328,
  case_prop = 0.035,
  rsq_exposure = 0.068,
  n_variants = 196,
  ols_bias = 0.2,
  overlap_prop = 0.3
)

# Continuous outcome
estimate_overlap_bias(
  samplesize_exposure = 361194,
  samplesize_outcome = 1125328,
  rsq_exposure = 0.068,
  n_variants = 196,
  ols_bias = 0.2,
  overlap_prop = 0.3
)