Gen.input: Generate model input

In AClement1990/hap-eQTL: What the Package Does (One Line, Title Case)

Description

This function prepares the input files for downstream analysis including annotating variants according to genes within which they fall. An RData object is created so that this function only needs to be run once.

Usage

Gen.input(
  ASE_file,
  legend_file,
  haplotypes_file,
  samples_file,
  output_prefix,
  species = "hsapiens",
  ensembl_version = NULL
)

Arguments

ASE_file	Specify file containing allele-specific expression information
legend_file	Specify legend file containing SNP IDs and position info etc
haplotypes_file	Provide haplotypes corresponding to SNPs in legend file, for given individuals found in samples file
samples_file	containing cohort information
output_prefix	Pre-fix to the name of the output file
species	Select same species as cohort. Defaults to 'hsapiens'
ensembl_version	Specify version of Ensembl to download from. Defaults to NULL which is the most recent build

Examples

#' #Annotating the input files using the most recent human gene set 
Gen.input('path_to_ASE_file/ASEfile.txt.gz',
                    'path_to_legend_file/file.legendfile.gz',
                   'path_to_haplotypes_file/hapfile.hap.gz',
                    'path_to_samples_file/samples.txt')
                    
#Annotating the input files using a previous human gene set
Gen.input('path_to_ASE_file/ASEfile.txt.gz',
                    'path_to_legend_file/file.legendfile.gz',
                   'path_to_haplotypes_file/hapfile.hap.gz',
                    'path_to_samples_file/samples.txt', ensembl_version=78)

#Annotating the input files using the most recent mouse gene set
Gen.input('path_to_ASE_file/ASEfile.txt.gz',
                    'path_to_legend_file/file.legendfile.gz',
                  'path_to_haplotypes_file/hapfile.hap.gz',
                    'path_to_samples_file/samples.txt',
                    'mmusculus')

AClement1990/hap-eQTL documentation built on Jan. 8, 2021, 12:41 a.m.