check_dataset: check_dataset

In coloc: Colocalisation Tests of Two Genetic Traits

check_dataset

Description

Check coloc dataset inputs for errors

Usage

check_dataset(d, suffix = "", req = c("type", "snp"), warn.minp = 1e-06)

check.dataset(...)

Arguments

d	dataset to check
suffix	string to identify which dataset (1 or 2)
req	names of elements that must be present
warn.minp	print warning if no p value < warn.minp
...	arguments passed to check_dataset()

Details

A coloc dataset is a list, containing a mixture of vectors capturing quantities that vary between snps (these vectors must all have equal length) and scalars capturing quantities that describe the dataset.

Coloc is flexible, requiring perhaps only p values, or z scores, or effect estimates and standard errors, but with this flexibility, also comes difficulties describing exactly the combinations of items required.

Required vectors are some subset of

beta

regression coefficient for each SNP from dataset 1

varbeta

variance of beta

pvalues

P-values for each SNP in dataset 1

MAF

minor allele frequency of the variants

snp

a character vector of snp ids, optional. It will be used to merge dataset1 and dataset2 and will be retained in the results.

Preferably, give beta and varbeta. But if these are not available, sufficient statistics can be approximated from pvalues and MAF.

Required scalars are some subset of

N

Number of samples in dataset 1

type

the type of data in dataset 1 - either "quant" or "cc" to denote quantitative or case-control

s

for a case control dataset, the proportion of samples in dataset 1 that are cases

sdY

for a quantitative trait, the population standard deviation of the trait. if not given, it can be estimated from the vectors of varbeta and MAF

You must always give type. Then,

if type=="cc"

s

if type=="quant" and sdY known

sdY

if beta, varbeta not known

N

If sdY is unknown, it will be approximated, and this will require

summary data to estimate sdY

beta, varbeta, N, MAF

Optional vectors are

position

a vector of snp positions, required for plot_dataset

check_dataset calls stop() unless a series of expectations on dataset input format are met

This is a helper function for use by other coloc functions, but you can use it directly to check the format of a dataset to be supplied to coloc.abf(), coloc.signals(), finemap.abf(), or finemap.signals().

Value

NULL if no errors found

Author(s)

Chris Wallace

coloc documentation built on Oct. 3, 2023, 5:07 p.m.