make_mamba_summary_files: Create input datasets for mamba() function and clumping Take...
In dan11mcguire/mamba: MAMBA: Meta-analysis Model Based Assessment of Replicability

Description Usage Arguments Value Examples

View source: R/make_mamba_summary_files.R

Create input datasets for mamba() function and clumping

Take gwas summary stat files, do ivw-meta-analysis, create an assoc dataset which could be used for clumping association statistics in plink, create beta and s2 input datasets for mamba() model

make_mamba_summary_files(summary_files,
  standardize_beta_and_s2_datasets = TRUE, beta_name = "b",
  s2_name = "s2", n_name = "n", af_name = "af", ref_name = "ref",
  alt_name = "alt", chr_name = "chr", bp_name = "bp")

`summary_files`	A list of summary statistic files with common column names
`standardize_beta_and_s2_datasets`	in the outputted b and s2 data tables, do you want the effect size estimates and variances standardized (i.e. beta = beta_ksqrt(2af_k*(1-af_k)))? Default is TRUE.
`beta_name`	name of effect size estimate column
`s2_name`	name of effect size variance estimate column
`n_name`	name of n column
`af_name`	name of af column
`ref_name`	name of reference allele column
`alt_name`	name of alt allele column
`chr_name`	name of chr column
`bp_name`	name of bp column

a list of three data.tables (beta, s2, and assoc)

 ## Not run: 
    datadir<-system.file("extdata", package="mamba")
    datafiles<-paste0(datadir, "/", list.files(datadir))
    looky<-make_mamba_summary_files(summary_files=datafiles, 
                             standardize_beta_and_s2_datasets=TRUE,
                             beta_name="betaj", s2_name="sj2")
    looky$assoc[1:5]
    looky$b[1:5] 
    looky$s2[1:5]

## End(Not run)