standardize: Standardize the locus subset

In RajLabMSSM/echodata: echoverse module: Fine-mapping data access and formatting

Standardize the locus subset

Description

After querying a subset of the full summary statistics, this function converts it into a standardized format that the rest of echolocatoR can work with.

Usage

standardize(
  query,
  subset_path = NULL,
  locus = NULL,
  colmap = construct_colmap(),
  compute_n = "ldsc",
  return_dt = TRUE,
  nThread = 1,
  verbose = TRUE
)

Arguments

query	data.frame of summary stat.
subset_path	Path where the query should be saved after standardization.
locus	Locus name.
colmap	Column mapping object created using construct_colmap.
compute_n	How to compute per-SNP sample size (new column "N"). If the column "N" is already present in dat, this column will be used to extract per-SNP sample sizes and the argument compute_n will be ignored. If the column "N" is not present in dat, one of the following options can be supplied to compute_n: 0: N will not be computed. >0: If any number >0 is provided, that value will be set as N for every row. **Note**: Computing N this way is incorrect and should be avoided if at all possible. "sum": N will be computed as: cases (N_CAS) + controls (N_CON), so long as both columns are present. "ldsc": N will be computed as effective sample size: Neff =(N_CAS+N_CON)*(N_CAS/(N_CAS+N_CON)) / mean((N_CAS/(N_CAS+N_CON))(N_CAS+N_CON)==max(N_CAS+N_CON)). "giant": N will be computed as effective sample size: Neff = 2 / (1/N_CAS + 1/N_CON). "metal": N will be computed as effective sample size: Neff = 4 / (1/N_CAS + 1/N_CON).
return_dt	Return data.table or path to saved data.table.
nThread	Number of threads to parallelise saving across.
verbose	Print messages.

Examples

query <- echodata::BST1
#### Screw up data
query$rsid <- query$SNP
query <- query[,-c("MAF","SNP")]
query[c(10,30,55),"Freq"] <- 0
query[c(12,22),"Freq"] <- NA 
subset_path <- file.path(tempdir(),"BST1.tsv")
colmap = construct_colmap(SNP="rsid")
query2 <- echodata::standardize(query = query,
                                subset_path = subset_path,
                                locus = "BST1",
                                colmap = colmap)

RajLabMSSM/echodata documentation built on Nov. 21, 2023, 8 a.m.