Gen.input: Generate model input

In AC1990/PackageTest:

Description

This function allows you to output .RData files to be used as input for the analysis run in the second function.

Usage

Gen.input(Chromosome, ASE_file, legend_file, haplotypes_file, Samples,
  output_path, Species = "hsapiens", EnsemblVersion = NULL)

Arguments

Chromosome	Specify chromosome
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_path	Directory path to save output files to
Species	Select same species as cohort. Defaults to "hsapiens"
EnsemblVersion	Specify version of Ensembl to download from. Defaults to NULL which is the most recent build

Examples

#Downloading Ensembl information for chromosome 22 of hsapiens, using the build corresponding to the sample data
Gen.input(22, "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", EnsemblVersion=78)

#Downloading Ensembl information for chromosome 22 of hsapiens, using the most recent build 
Gen.input(22, "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")

#Downloading Ensembl information for chromosome 1 of mmusculus, using the most recent build
Gen.input(1, "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")

AC1990/PackageTest documentation built on Dec. 2, 2020, 10:08 a.m.