Format input

This function takes input and output files of TensorQTL and returns a list object that can be used as input for do_bms. It currenly only handles completely unpaired data, where there is no repeated measurement per donor (subject). This includes typical molecular data from clinical trials.

format_input(
  qtl,
  pheno,
  geno,
  covar,
  int,
  pheno.col = "phenotype_id",
  variant.col = "variant_id",
  feat.col = "gene_id",
  snp.col = "SNP",
  pheno.rm = 1:4,
  geno.rm = 1:6
)

Arguments

qtl

A character string specfying the name of the output file from interacton QTL mapping from TensorQTL.

pheno

A character string specifynig the name of the file containing molecular phenotes. This must be the same as the input file used for TensorQTL.

geno

A character string specifying the name of the genotype file in PLINK2 .traw format.

covar

A character string specifyng the name of the file containing covariates. This must be the same as the input file used for TensorQTL.

int

A character string specifying the name of the file containing the condition variable of interest, coded as 1 and 2. This must be the same as the input file used for TensorQTL.

pheno.col

A character string specifying the name of the column of qtl containing the feature IDs.

variant.col

A character string specifying the name of the column of qtl containing the feature IDs.

feat.col

A character string specifying the name of the column of pheno containing the feature IDs.

snp.col

A character string specifying the name of the column of geno containing the SNP IDs.

pheno.rm

A vector of integers corresponding to the column numbers for non-phenotype entries in pheno.

geno.rm

A vector of integers corresponding to the column numbers for non-phenotype entries in geno.

Value

A list of lists containing:

• y - A vector of phenotypes.

• g - A vector of genotypes.

• t - A vector of treatment indicators.

• subject - A vector of subject.

• feat.id - A character string spcifyng the feature ID.

• snp.id - A character string specifying the SNP ID.