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Run a TWAS using S-PrediXcan

Source: R/s_predixcan.R
s_predixcan.Rd

This function is a wrapper around S-PrediXcan, a method of integrating GWAS summary statistics with gene-expression/splicing data to identify genes associated with a trait. The PrediXcan/MetaXcan method is described in Barbeira et al. (Nature Communications 2018; https://doi.org/10.1038/s41467-018-03621-1). The MetaXcan tools can be found on Github (https://github.com/hakyimlab/MetaXcan) and PredictDB (https://predictdb.org/). If S-PrediXcan is run across multiple tissues, the results can be integrated using s_multixcan().

Usage

s_predixcan(
  df,
  snp = SNP,
  effect_allele = effect_allele,
  other_allele = other_allele,
  beta = beta,
  eaf = eaf,
  chr = chr,
  pos = pos,
  se = se,
  pval = pval,
  samplesize = samplesize,
  data,
  metaxcan,
  output,
  model_db_path,
  model_covariance_path,
  trait_name
)

Arguments

df

Dataframe containing GWAS summary statistics

snp

Column containing rsid

effect_allele

Column containing effect allele

other_allele

Column containing non-effect allele

beta

Column containing effect size

eaf

Column containing effect allele frequency

chr

Column containing chromosome

pos

Column containing position

se

Column containing standard error of the effect estimate

pval

Column containing p-value

samplesize

Column containing samplesize

data

Path to MetaXcan data (eg. "MetaXcan/data")

metaxcan

Path to MetaXcan (eg. "MetaXcan/software")

output

Output directory to save S-PrediXcan results

model_db_path

Path to PrediXcan model database

model_covariance_path

Path to PrediXcan model covariance

trait_name

Name of GWAS trait (used to name output files)

Value

A dataframe containing the S-PrediXcan results

See also

Other TWAS: s_multixcan()

Other Gene-based testing: magmar(), s_multixcan()

Examples

if (FALSE) {
s_predixcan(df, data = "MetaXcan/data", metaxcan = "MetaXcan/software", output = "/path/to/output", model_db_path = "MetaXcan/data/models/eqtl/mashr/mashr_Liver.db", model_covariance_path = "MetaXcan/data/models/eqtl/mashr/mashr_Liver.txt.gz", trait_name = "GWAS_trait")
}