SIP (version 0.1.0)

sip_pair: Single-iteration paired permutation for large-scale biobank data with relatedness

Description

# This function performs paired permutation for permuting phenotype vectors among related individuals in biobank data.

Usage

sip_pair(
  df = NULL,
  id.var = NULL,
  sex.var = NULL,
  male.val = NULL,
  female.val = NULL,
  geno.vars = NULL,
  within.sex = TRUE,
  seed = NULL,
  rel.df = NULL,
  rid.vars = NULL,
  ibd.var = NULL
)

Value

Data frame

Arguments

df, rel.df

Data frame

id.var, sex.var, ibd.var

Strings

male.val, female.val

Strings or integers

geno.vars, rid.vars

Character vectors

within.sex

Boolean, defaults to TRUE

seed

Number

Details

The function requires the following inputs:

1) A sample-by-variable data frame with phenotypes and covariates. Column names should include an ID variable, sex variable, genotypic covariate names, phenotypic covariate names, and phenotype names. (N.B. a secondary ID variable can be included in the genotypic covariate names.)

2) A string identifying the ID variable name (e.g., id.var="ID").

3) A vector of genotypic covariates (e.g., geno.vars=c("ID2","Batch","PC1","PC2",...)).

4) A relatedness data frame containing identity-by-descent (IBD) for pairs of individuals in the sample-by-variable data frame. Column names should include two ID variables and an IBD variable.

5) A vector of the 2 ID variable names in the relatedness data frame. (e.g., rid.vars=c("ID1","ID2")).

6) A string identifying the IBD variable name (e.g., ibd.var="PropIBD").

7) Optional: within.sex = FALSE. Default is within.sex = TRUE and will permute males and females separately.

8) If within.sex = TRUE (the default), a string identifying the sex variable name (e.g., sex.var="Inferred_Sex").

9) If within.sex = TRUE (the default), male and female values in the sex vector (e.g., male.val=1, female.val=2).

10) Optional: a seed for sampling. If a seed is not provided, one will be chosen randomly during the sampling process (e.g., seed=123).

11) N.B. Any column names not specified in (2)-(9) are assumed to be phenotypes or phenotypic covariates.

Examples

sip_pair(df = sipPair_exampleData, id.var = "IID",
sex.var = "SEX", male.val = "M", female.val = "F",
geno.vars = c("FID","BATCH",paste0("PC",1:4)),
rel.df = sipPair_relatednessData, rid.vars=c("IID1","IID2"),
ibd.var="PropIBD")