Check coloc dataset inputs for errors
check_dataset(d, suffix = "", req = c("type", "snp"), warn.minp = 1e-06)
check.dataset(...)dataset to check
string to identify which dataset (1 or 2)
names of elements that must be present
print warning if no p value < warn.minp
arguments passed to check_dataset()
NULL if no errors found
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
regression coefficient for each SNP from dataset 1
variance of beta
P-values for each SNP in dataset 1
minor allele frequency of the variants
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
Number of samples in dataset 1
the type of data in dataset 1 - either "quant" or "cc" to denote quantitative or case-control
for a case control dataset, the proportion of samples in dataset 1 that are cases
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,
type=="cc"s
type=="quant" and sdY knownsdY
N
If sdY is unknown, it will be approximated, and this will require
sdYbeta, varbeta, N, MAF
Optional vectors are
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().