Convert from MungeSumstats to echolocatoR format

Source: R/mungesumstats_to_echolocatoR.R

Convert column names between package-specific formats. Optionally, can also be used to first automatically standardise column names by setting standardise_colnames=TRUE before converting to echolocatoR format.

mungesumstats_to_echolocatoR(dat, standardise_colnames = FALSE, verbose = TRUE)

Arguments

dat

A data.table of SNP-level summary statistics.

standardise_colnames

Automatically rename all columns to a standard nomenclature using standardise_header.

verbose

Print messages.

Examples

 
dat <- dplyr::rename(echodata::BST1, BPOS=POS, SEBETA=StdErr, B=Effect)
dat_echoR <- echodata::mungesumstats_to_echolocatoR(
    dat=dat,
    standardise_colnames=TRUE)
#> + Mapping colnames from MungeSumstats ==> echolocatoR
#> Standardising column headers.
#> First line of summary statistics file: 
#> SNP	CHR	BPOS	P	B	SEBETA	Freq	MAF	N_cases	N_controls	proportion_cases	A1	A2	leadSNP	ABF.CS	ABF.PP	SUSIE.CS	SUSIE.PP	POLYFUN_SUSIE.CS	POLYFUN_SUSIE.PP	FINEMAP.CS	FINEMAP.PP	Support	Consensus_SNP	mean.PP	mean.CS